Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c14b' (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/6709339-fedora-39-x86_64 --chroot fedora-39-x86_64 Version: 0.70 PID: 5966 Logging PID: 5967 Task: {'appstream': False, 'background': True, 'build_id': 6709339, 'buildroot_pkgs': [], 'chroot': 'fedora-39-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'bdf50a409fce8a5edcb19279c65d97699236b9f6', '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': '0.22.0-2', 'project_dirname': 'setuptools-impact-check-control', 'project_name': 'setuptools-impact-check-control', 'project_owner': 'thrnciar', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/thrnciar/setuptools-impact-check-control/fedora-39-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'thrnciar/setuptools-impact-check-control--https://src.fedoraproject.org/user/fweimer', 'source_json': {}, 'source_type': None, 'submitter': 'https://src.fedoraproject.org/user/fweimer', 'tags': [], 'task_id': '6709339-fedora-39-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/thrnciar/setuptools-impact-check-control/python-pysam /var/lib/copr-rpmbuild/workspace/workdir-rk9y605x/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-rk9y605x/python-pysam', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-rk9y605x/python-pysam'... Running: git checkout bdf50a409fce8a5edcb19279c65d97699236b9f6 -- cmd: ['git', 'checkout', 'bdf50a409fce8a5edcb19279c65d97699236b9f6', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-rk9y605x/python-pysam rc: 0 stdout: stderr: Note: switching to 'bdf50a409fce8a5edcb19279c65d97699236b9f6'. 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 bdf50a4 automatic import of python-pysam Running: copr-distgit-client sources /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-rk9y605x/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 100 4522k 100 4522k 0 0 24.5M 0 --:--:-- --:--:-- --:--:-- 24.5M INFO: Reading stdout from command: md5sum pysam-0.22.0.tar.gz Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-rk9y605x/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-rk9y605x/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1701370364.023813 -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-rk9y605x/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-rk9y605x/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1701370364.023813 -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-rk9y605x/python-pysam/python-pysam.spec) Config(fedora-39-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-39-x86_64-bootstrap-1701370364.023813/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:39 INFO: Pulling image: registry.fedoraproject.org/fedora:39 INFO: Copy content of container registry.fedoraproject.org/fedora:39 to /var/lib/mock/fedora-39-x86_64-bootstrap-1701370364.023813/root INFO: Checking that registry.fedoraproject.org/fedora:39 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:39 with podman image mount INFO: image registry.fedoraproject.org/fedora:39 as /var/lib/containers/storage/overlay/8ff7ad910417a7b8a49019008335921d2aac0e3304a19ce258deabf431e59801/merged INFO: umounting image registry.fedoraproject.org/fedora:39 (/var/lib/containers/storage/overlay/8ff7ad910417a7b8a49019008335921d2aac0e3304a19ce258deabf431e59801/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 11 MB/s | 1.7 MB 00:00 fedora 152 kB/s | 89 MB 10:01 updates 6.8 MB/s | 17 MB 00:02 Last metadata expiration check: 0:00:01 ago on Thu Nov 30 19:03:14 2023. Package python3-dnf-4.18.1-2.fc39.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-dnf-plugins-core noarch 4.4.3-1.fc39 updates 317 k Installing dependencies: dbus-libs x86_64 1:1.14.10-1.fc39 fedora 156 k python3-dateutil noarch 1:2.8.2-10.fc39 fedora 355 k python3-dbus x86_64 1.3.2-4.fc39 fedora 157 k python3-distro noarch 1.8.0-6.fc39 fedora 49 k python3-six noarch 1.16.0-12.fc39 fedora 41 k python3-systemd x86_64 235-5.fc39 fedora 107 k Transaction Summary ================================================================================ Install 7 Packages Total download size: 1.2 M Installed size: 3.6 M Downloading Packages: (1/7): dbus-libs-1.14.10-1.fc39.x86_64.rpm 249 kB/s | 156 kB 00:00 (2/7): python3-dbus-1.3.2-4.fc39.x86_64.rpm 231 kB/s | 157 kB 00:00 (3/7): python3-distro-1.8.0-6.fc39.noarch.rpm 278 kB/s | 49 kB 00:00 (4/7): python3-six-1.16.0-12.fc39.noarch.rpm 333 kB/s | 41 kB 00:00 (5/7): python3-dateutil-2.8.2-10.fc39.noarch.rp 397 kB/s | 355 kB 00:00 (6/7): python3-systemd-235-5.fc39.x86_64.rpm 934 kB/s | 107 kB 00:00 (7/7): python3-dnf-plugins-core-4.4.3-1.fc39.no 2.0 MB/s | 317 kB 00:00 -------------------------------------------------------------------------------- Total 1.1 MB/s | 1.2 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-systemd-235-5.fc39.x86_64 1/7 Installing : python3-six-1.16.0-12.fc39.noarch 2/7 Installing : python3-dateutil-1:2.8.2-10.fc39.noarch 3/7 Installing : python3-distro-1.8.0-6.fc39.noarch 4/7 Installing : dbus-libs-1:1.14.10-1.fc39.x86_64 5/7 Installing : python3-dbus-1.3.2-4.fc39.x86_64 6/7 Installing : python3-dnf-plugins-core-4.4.3-1.fc39.noarch 7/7 Running scriptlet: python3-dnf-plugins-core-4.4.3-1.fc39.noarch 7/7 Verifying : dbus-libs-1:1.14.10-1.fc39.x86_64 1/7 Verifying : python3-dateutil-1:2.8.2-10.fc39.noarch 2/7 Verifying : python3-dbus-1.3.2-4.fc39.x86_64 3/7 Verifying : python3-distro-1.8.0-6.fc39.noarch 4/7 Verifying : python3-six-1.16.0-12.fc39.noarch 5/7 Verifying : python3-systemd-235-5.fc39.x86_64 6/7 Verifying : python3-dnf-plugins-core-4.4.3-1.fc39.noarch 7/7 Installed: dbus-libs-1:1.14.10-1.fc39.x86_64 python3-dateutil-1:2.8.2-10.fc39.noarch python3-dbus-1.3.2-4.fc39.x86_64 python3-distro-1.8.0-6.fc39.noarch python3-dnf-plugins-core-4.4.3-1.fc39.noarch python3-six-1.16.0-12.fc39.noarch python3-systemd-235-5.fc39.x86_64 Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1701370364.023813/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 11 MB/s | 1.7 MB 00:00 fedora 12 MB/s | 89 MB 00:07 updates 1.5 MB/s | 17 MB 00:11 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash x86_64 5.2.21-1.fc39 updates 1.8 M bzip2 x86_64 1.0.8-16.fc39 fedora 52 k coreutils x86_64 9.3-4.fc39 fedora 1.1 M cpio x86_64 2.14-4.fc39 fedora 279 k diffutils x86_64 3.10-3.fc39 fedora 398 k fedora-release-common noarch 39-34 updates 19 k findutils x86_64 1:4.9.0-5.fc39 fedora 492 k gawk x86_64 5.2.2-2.fc39 fedora 1.1 M glibc-minimal-langpack x86_64 2.38-11.fc39 updates 70 k grep x86_64 3.11-3.fc39 fedora 298 k gzip x86_64 1.12-6.fc39 fedora 166 k info x86_64 7.0.3-3.fc39 fedora 182 k patch x86_64 2.7.6-22.fc39 fedora 125 k redhat-rpm-config noarch 262-1.fc39 fedora 84 k rpm-build x86_64 4.19.0-1.fc39 fedora 78 k sed x86_64 4.8-14.fc39 fedora 306 k shadow-utils x86_64 2:4.14.0-2.fc39 updates 1.3 M tar x86_64 2:1.35-2.fc39 fedora 864 k unzip x86_64 6.0-62.fc39 fedora 184 k util-linux x86_64 2.39.2-1.fc39 fedora 1.2 M which x86_64 2.21-40.fc39 fedora 42 k xz x86_64 5.4.4-1.fc39 fedora 556 k Installing dependencies: alternatives x86_64 1.25-1.fc39 fedora 39 k ansible-srpm-macros noarch 1-11.fc39 fedora 21 k audit-libs x86_64 3.1.2-5.fc39 updates 117 k authselect x86_64 1.4.3-1.fc39 fedora 149 k authselect-libs x86_64 1.4.3-1.fc39 fedora 249 k basesystem noarch 11-18.fc39 fedora 7.2 k binutils x86_64 2.40-13.fc39 fedora 5.6 M binutils-gold x86_64 2.40-13.fc39 fedora 797 k bzip2-libs x86_64 1.0.8-16.fc39 fedora 41 k ca-certificates noarch 2023.2.60_v7.0.306-2.fc39 fedora 837 k coreutils-common x86_64 9.3-4.fc39 fedora 2.1 M cracklib x86_64 2.9.11-2.fc39 fedora 94 k crypto-policies noarch 20231113-1.gitb402e82.fc39 updates 99 k curl x86_64 8.2.1-3.fc39 fedora 345 k cyrus-sasl-lib x86_64 2.1.28-11.fc39 fedora 793 k debugedit x86_64 5.0-10.fc39 fedora 77 k dwz x86_64 0.15-3.fc39 fedora 134 k ed x86_64 1.19-4.fc39 fedora 79 k efi-srpm-macros noarch 5-9.fc39 fedora 22 k elfutils x86_64 0.190-1.fc39 updates 550 k elfutils-debuginfod-client x86_64 0.190-1.fc39 updates 38 k elfutils-default-yama-scope noarch 0.190-1.fc39 updates 14 k elfutils-libelf x86_64 0.190-1.fc39 updates 195 k elfutils-libs x86_64 0.190-1.fc39 updates 260 k fedora-gpg-keys noarch 39-1 fedora 130 k fedora-release noarch 39-34 updates 8.4 k fedora-release-identity-basic noarch 39-34 updates 9.2 k fedora-repos noarch 39-1 fedora 9.3 k file x86_64 5.44-5.fc39 fedora 49 k file-libs x86_64 5.44-5.fc39 fedora 729 k filesystem x86_64 3.18-6.fc39 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-12.fc39 fedora 26 k fpc-srpm-macros noarch 1.3-8.fc39 fedora 7.4 k gdb-minimal x86_64 13.2-10.fc39 updates 4.2 M gdbm-libs x86_64 1:1.23-4.fc39 fedora 56 k ghc-srpm-macros noarch 1.6.1-2.fc39 fedora 7.8 k glibc x86_64 2.38-11.fc39 updates 2.2 M glibc-common x86_64 2.38-11.fc39 updates 351 k glibc-gconv-extra x86_64 2.38-11.fc39 updates 1.6 M gmp x86_64 1:6.2.1-5.fc39 fedora 313 k gnat-srpm-macros noarch 6-3.fc39 fedora 8.8 k go-srpm-macros noarch 3.3.1-1.fc39 updates 28 k jansson x86_64 2.13.1-7.fc39 fedora 44 k kernel-srpm-macros noarch 1.0-20.fc39 fedora 10 k keyutils-libs x86_64 1.6.1-7.fc39 fedora 31 k krb5-libs x86_64 1.21.2-2.fc39 updates 764 k libacl x86_64 2.3.1-8.fc39 fedora 23 k libarchive x86_64 3.7.1-1.fc39 fedora 408 k libattr x86_64 2.5.1-8.fc39 fedora 18 k libblkid x86_64 2.39.2-1.fc39 fedora 116 k libbrotli x86_64 1.1.0-1.fc39 fedora 336 k libcap x86_64 2.48-8.fc39 updates 68 k libcap-ng x86_64 0.8.3-8.fc39 fedora 32 k libcom_err x86_64 1.47.0-2.fc39 fedora 26 k libcurl x86_64 8.2.1-3.fc39 fedora 323 k libdb x86_64 5.3.28-56.fc39 fedora 760 k libeconf x86_64 0.5.2-1.fc39 fedora 30 k libevent x86_64 2.1.12-9.fc39 fedora 258 k libfdisk x86_64 2.39.2-1.fc39 fedora 162 k libffi x86_64 3.4.4-4.fc39 fedora 40 k libgcc x86_64 13.2.1-4.fc39 updates 111 k libgomp x86_64 13.2.1-4.fc39 updates 320 k libidn2 x86_64 2.3.4-3.fc39 fedora 117 k libmount x86_64 2.39.2-1.fc39 fedora 155 k libnghttp2 x86_64 1.55.1-4.fc39 updates 76 k libnsl2 x86_64 2.0.0-6.fc39 fedora 30 k libpkgconf x86_64 1.9.5-2.fc39 fedora 38 k libpsl x86_64 0.21.2-4.fc39 fedora 63 k libpwquality x86_64 1.4.5-6.fc39 fedora 120 k libselinux x86_64 3.5-5.fc39 fedora 87 k libsemanage x86_64 3.5-4.fc39 fedora 120 k libsepol x86_64 3.5-2.fc39 fedora 324 k libsigsegv x86_64 2.14-5.fc39 fedora 27 k libsmartcols x86_64 2.39.2-1.fc39 fedora 67 k libssh x86_64 0.10.5-2.fc39 fedora 211 k libssh-config noarch 0.10.5-2.fc39 fedora 9.2 k libstdc++ x86_64 13.2.1-4.fc39 updates 862 k libtasn1 x86_64 4.19.0-3.fc39 fedora 74 k libtirpc x86_64 1.3.4-0.fc39 updates 94 k libunistring x86_64 1.1-5.fc39 fedora 543 k libutempter x86_64 1.2.1-10.fc39 fedora 26 k libuuid x86_64 2.39.2-1.fc39 fedora 28 k libverto x86_64 0.3.2-6.fc39 fedora 20 k libxcrypt x86_64 4.4.36-2.fc39 fedora 119 k libxml2 x86_64 2.10.4-3.fc39 fedora 701 k libzstd x86_64 1.5.5-4.fc39 fedora 309 k lua-libs x86_64 5.4.6-3.fc39 fedora 133 k lua-srpm-macros noarch 1-9.fc39 fedora 8.6 k lz4-libs x86_64 1.9.4-4.fc39 fedora 67 k mpfr x86_64 4.2.0-3.fc39 fedora 344 k ncurses-base noarch 6.4-7.20230520.fc39 fedora 88 k ncurses-libs x86_64 6.4-7.20230520.fc39 fedora 336 k ocaml-srpm-macros noarch 8-2.fc39 fedora 14 k openblas-srpm-macros noarch 2-14.fc39 fedora 7.5 k openldap x86_64 2.6.6-1.fc39 fedora 255 k openssl-libs x86_64 1:3.1.1-4.fc39 fedora 2.2 M p11-kit x86_64 0.25.3-1.fc39 updates 520 k p11-kit-trust x86_64 0.25.3-1.fc39 updates 140 k package-notes-srpm-macros noarch 0.5-9.fc39 fedora 11 k pam x86_64 1.5.3-3.fc39 updates 542 k pam-libs x86_64 1.5.3-3.fc39 updates 56 k pcre2 x86_64 10.42-1.fc39.2 fedora 233 k pcre2-syntax noarch 10.42-1.fc39.2 fedora 143 k perl-srpm-macros noarch 1-51.fc39 fedora 8.0 k pkgconf x86_64 1.9.5-2.fc39 fedora 42 k pkgconf-m4 noarch 1.9.5-2.fc39 fedora 14 k pkgconf-pkg-config x86_64 1.9.5-2.fc39 fedora 9.6 k popt x86_64 1.19-3.fc39 fedora 66 k publicsuffix-list-dafsa noarch 20230812-1.fc39 fedora 57 k pyproject-srpm-macros noarch 1.10.0-1.fc39 updates 14 k python-srpm-macros noarch 3.12-4.fc39 fedora 25 k qt5-srpm-macros noarch 5.15.11-1.fc39 updates 8.3 k qt6-srpm-macros noarch 6.6.0-1.fc39 updates 8.6 k readline x86_64 8.2-4.fc39 fedora 213 k rpm x86_64 4.19.0-1.fc39 fedora 538 k rpm-build-libs x86_64 4.19.0-1.fc39 fedora 96 k rpm-libs x86_64 4.19.0-1.fc39 fedora 312 k rpm-sequoia x86_64 1.5.0-1.fc39 fedora 871 k rpmautospec-rpm-macros noarch 0.3.8-1.fc39 updates 9.0 k rust-srpm-macros noarch 25.2-2.fc39 updates 13 k setup noarch 2.14.4-1.fc39 fedora 154 k sqlite-libs x86_64 3.42.0-7.fc39 fedora 678 k systemd-libs x86_64 254.5-2.fc39 fedora 689 k util-linux-core x86_64 2.39.2-1.fc39 fedora 494 k xxhash-libs x86_64 0.8.2-1.fc39 fedora 37 k xz-libs x86_64 5.4.4-1.fc39 fedora 108 k zip x86_64 3.0-39.fc39 fedora 266 k zlib x86_64 1.2.13-4.fc39 fedora 94 k zstd x86_64 1.5.5-4.fc39 fedora 482 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 151 Packages Total download size: 52 M Installed size: 178 M Downloading Packages: (1/151): ansible-srpm-macros-1-11.fc39.noarch.r 284 kB/s | 21 kB 00:00 (2/151): alternatives-1.25-1.fc39.x86_64.rpm 464 kB/s | 39 kB 00:00 (3/151): basesystem-11-18.fc39.noarch.rpm 359 kB/s | 7.2 kB 00:00 (4/151): authselect-1.4.3-1.fc39.x86_64.rpm 1.2 MB/s | 149 kB 00:00 (5/151): authselect-libs-1.4.3-1.fc39.x86_64.rp 2.8 MB/s | 249 kB 00:00 (6/151): bzip2-1.0.8-16.fc39.x86_64.rpm 2.5 MB/s | 52 kB 00:00 (7/151): binutils-gold-2.40-13.fc39.x86_64.rpm 11 MB/s | 797 kB 00:00 (8/151): bzip2-libs-1.0.8-16.fc39.x86_64.rpm 1.9 MB/s | 41 kB 00:00 (9/151): ca-certificates-2023.2.60_v7.0.306-2.f 21 MB/s | 837 kB 00:00 (10/151): coreutils-common-9.3-4.fc39.x86_64.rp 19 MB/s | 2.1 MB 00:00 (11/151): coreutils-9.3-4.fc39.x86_64.rpm 6.8 MB/s | 1.1 MB 00:00 (12/151): binutils-2.40-13.fc39.x86_64.rpm 21 MB/s | 5.6 MB 00:00 (13/151): cracklib-2.9.11-2.fc39.x86_64.rpm 2.5 MB/s | 94 kB 00:00 (14/151): cpio-2.14-4.fc39.x86_64.rpm 2.8 MB/s | 279 kB 00:00 (15/151): cyrus-sasl-lib-2.1.28-11.fc39.x86_64. 16 MB/s | 793 kB 00:00 (16/151): curl-8.2.1-3.fc39.x86_64.rpm 3.9 MB/s | 345 kB 00:00 (17/151): debugedit-5.0-10.fc39.x86_64.rpm 3.9 MB/s | 77 kB 00:00 (18/151): diffutils-3.10-3.fc39.x86_64.rpm 14 MB/s | 398 kB 00:00 (19/151): dwz-0.15-3.fc39.x86_64.rpm 5.4 MB/s | 134 kB 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-------------------------------------------------------------------------------- Total 15 MB/s | 52 MB 00:03 fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x18B8E74C: Userid : "Fedora (39) " Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-6.fc39.x86_64 1/1 Preparing : 1/1 Installing : libgcc-13.2.1-4.fc39.x86_64 1/151 Running scriptlet: libgcc-13.2.1-4.fc39.x86_64 1/151 Installing : crypto-policies-20231113-1.gitb402e82.fc39.noarc 2/151 Running scriptlet: crypto-policies-20231113-1.gitb402e82.fc39.noarc 2/151 Installing : fedora-release-identity-basic-39-34.noarch 3/151 Installing : fedora-gpg-keys-39-1.noarch 4/151 Installing : fedora-repos-39-1.noarch 5/151 Installing : fedora-release-common-39-34.noarch 6/151 Installing : fedora-release-39-34.noarch 7/151 Installing : setup-2.14.4-1.fc39.noarch 8/151 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.4-1.fc39.noarch 8/151 Installing : filesystem-3.18-6.fc39.x86_64 9/151 Installing : basesystem-11-18.fc39.noarch 10/151 Installing : rust-srpm-macros-25.2-2.fc39.noarch 11/151 Installing : qt6-srpm-macros-6.6.0-1.fc39.noarch 12/151 Installing : qt5-srpm-macros-5.15.11-1.fc39.noarch 13/151 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Installing : unzip-6.0-62.fc39.x86_64 48/151 Installing : file-libs-5.44-5.fc39.x86_64 49/151 Installing : file-5.44-5.fc39.x86_64 50/151 Installing : alternatives-1.25-1.fc39.x86_64 51/151 Installing : jansson-2.13.1-7.fc39.x86_64 52/151 Installing : libcap-ng-0.8.3-8.fc39.x86_64 53/151 Installing : audit-libs-3.1.2-5.fc39.x86_64 54/151 Installing : pam-libs-1.5.3-3.fc39.x86_64 55/151 Installing : libcom_err-1.47.0-2.fc39.x86_64 56/151 Installing : libsepol-3.5-2.fc39.x86_64 57/151 Installing : libsmartcols-2.39.2-1.fc39.x86_64 58/151 Installing : libtasn1-4.19.0-3.fc39.x86_64 59/151 Installing : libunistring-1.1-5.fc39.x86_64 60/151 Installing : libidn2-2.3.4-3.fc39.x86_64 61/151 Installing : lua-libs-5.4.6-3.fc39.x86_64 62/151 Installing : pcre2-10.42-1.fc39.2.x86_64 63/151 Installing : libselinux-3.5-5.fc39.x86_64 64/151 Installing : sed-4.8-14.fc39.x86_64 65/151 Installing : grep-3.11-3.fc39.x86_64 66/151 Installing : findutils-1:4.9.0-5.fc39.x86_64 67/151 Installing : 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cyrus-sasl-lib-2.1.28-11.fc39.x86_64 87/151 Installing : keyutils-libs-1.6.1-7.fc39.x86_64 88/151 Installing : libbrotli-1.1.0-1.fc39.x86_64 89/151 Installing : libdb-5.3.28-56.fc39.x86_64 90/151 Installing : libffi-3.4.4-4.fc39.x86_64 91/151 Installing : p11-kit-0.25.3-1.fc39.x86_64 92/151 Installing : p11-kit-trust-0.25.3-1.fc39.x86_64 93/151 Running scriptlet: p11-kit-trust-0.25.3-1.fc39.x86_64 93/151 Installing : libpkgconf-1.9.5-2.fc39.x86_64 94/151 Installing : pkgconf-1.9.5-2.fc39.x86_64 95/151 Installing : pkgconf-pkg-config-1.9.5-2.fc39.x86_64 96/151 Installing : libsigsegv-2.14-5.fc39.x86_64 97/151 Installing : gawk-5.2.2-2.fc39.x86_64 98/151 Installing : libverto-0.3.2-6.fc39.x86_64 99/151 Installing : xxhash-libs-0.8.2-1.fc39.x86_64 100/151 Installing : libgomp-13.2.1-4.fc39.x86_64 101/151 Installing : libnghttp2-1.55.1-4.fc39.x86_64 102/151 Installing : elfutils-default-yama-scope-0.190-1.fc39.noarch 103/151 Running scriptlet: elfutils-default-yama-scope-0.190-1.fc39.noarch 103/151 Installing : libssh-config-0.10.5-2.fc39.noarch 104/151 Installing : kernel-srpm-macros-1.0-20.fc39.noarch 105/151 Installing : gnat-srpm-macros-6-3.fc39.noarch 106/151 Installing : ghc-srpm-macros-1.6.1-2.fc39.noarch 107/151 Installing : fpc-srpm-macros-1.3-8.fc39.noarch 108/151 Installing : coreutils-common-9.3-4.fc39.x86_64 109/151 Installing : openssl-libs-1:3.1.1-4.fc39.x86_64 110/151 Installing : coreutils-9.3-4.fc39.x86_64 111/151 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 112/151 Installing : ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 112/151 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 112/151 Installing : krb5-libs-1.21.2-2.fc39.x86_64 113/151 Installing : libtirpc-1.3.4-0.fc39.x86_64 114/151 Running scriptlet: authselect-libs-1.4.3-1.fc39.x86_64 115/151 Installing : authselect-libs-1.4.3-1.fc39.x86_64 115/151 Installing : gzip-1.12-6.fc39.x86_64 116/151 Installing : cracklib-2.9.11-2.fc39.x86_64 117/151 Installing : libpwquality-1.4.5-6.fc39.x86_64 118/151 Installing : authselect-1.4.3-1.fc39.x86_64 119/151 Installing : libnsl2-2.0.0-6.fc39.x86_64 120/151 Installing : pam-1.5.3-3.fc39.x86_64 121/151 Installing : libssh-0.10.5-2.fc39.x86_64 122/151 Installing : libarchive-3.7.1-1.fc39.x86_64 123/151 Installing : libevent-2.1.12-9.fc39.x86_64 124/151 Installing : openldap-2.6.6-1.fc39.x86_64 125/151 Installing : libcurl-8.2.1-3.fc39.x86_64 126/151 Installing : elfutils-libs-0.190-1.fc39.x86_64 127/151 Installing : elfutils-debuginfod-client-0.190-1.fc39.x86_64 128/151 Installing : binutils-gold-2.40-13.fc39.x86_64 129/151 Running scriptlet: binutils-gold-2.40-13.fc39.x86_64 129/151 Installing : binutils-2.40-13.fc39.x86_64 130/151 Running scriptlet: binutils-2.40-13.fc39.x86_64 130/151 Installing : elfutils-0.190-1.fc39.x86_64 131/151 Installing : gdb-minimal-13.2-10.fc39.x86_64 132/151 Installing : debugedit-5.0-10.fc39.x86_64 133/151 Installing : curl-8.2.1-3.fc39.x86_64 134/151 Installing : rpm-sequoia-1.5.0-1.fc39.x86_64 135/151 Installing : rpm-libs-4.19.0-1.fc39.x86_64 136/151 Running scriptlet: rpm-4.19.0-1.fc39.x86_64 137/151 Installing : rpm-4.19.0-1.fc39.x86_64 137/151 Installing : efi-srpm-macros-5-9.fc39.noarch 138/151 Installing : lua-srpm-macros-1-9.fc39.noarch 139/151 Installing : rpmautospec-rpm-macros-0.3.8-1.fc39.noarch 140/151 Installing : rpm-build-libs-4.19.0-1.fc39.x86_64 141/151 Installing : ansible-srpm-macros-1-11.fc39.noarch 142/151 Installing : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 143/151 Installing : python-srpm-macros-3.12-4.fc39.noarch 144/151 Installing : go-srpm-macros-3.3.1-1.fc39.noarch 145/151 Installing : redhat-rpm-config-262-1.fc39.noarch 146/151 Installing : rpm-build-4.19.0-1.fc39.x86_64 147/151 Installing : pyproject-srpm-macros-1.10.0-1.fc39.noarch 148/151 Installing : util-linux-2.39.2-1.fc39.x86_64 149/151 Installing : which-2.21-40.fc39.x86_64 150/151 Installing : info-7.0.3-3.fc39.x86_64 151/151 Running scriptlet: filesystem-3.18-6.fc39.x86_64 151/151 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 151/151 Running scriptlet: authselect-libs-1.4.3-1.fc39.x86_64 151/151 Running scriptlet: rpm-4.19.0-1.fc39.x86_64 151/151 Running scriptlet: info-7.0.3-3.fc39.x86_64 151/151 Verifying : alternatives-1.25-1.fc39.x86_64 1/151 Verifying : ansible-srpm-macros-1-11.fc39.noarch 2/151 Verifying : authselect-1.4.3-1.fc39.x86_64 3/151 Verifying : authselect-libs-1.4.3-1.fc39.x86_64 4/151 Verifying : basesystem-11-18.fc39.noarch 5/151 Verifying : binutils-2.40-13.fc39.x86_64 6/151 Verifying : binutils-gold-2.40-13.fc39.x86_64 7/151 Verifying : bzip2-1.0.8-16.fc39.x86_64 8/151 Verifying : bzip2-libs-1.0.8-16.fc39.x86_64 9/151 Verifying : ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch 10/151 Verifying : coreutils-9.3-4.fc39.x86_64 11/151 Verifying : coreutils-common-9.3-4.fc39.x86_64 12/151 Verifying : cpio-2.14-4.fc39.x86_64 13/151 Verifying : cracklib-2.9.11-2.fc39.x86_64 14/151 Verifying : curl-8.2.1-3.fc39.x86_64 15/151 Verifying : cyrus-sasl-lib-2.1.28-11.fc39.x86_64 16/151 Verifying : debugedit-5.0-10.fc39.x86_64 17/151 Verifying : diffutils-3.10-3.fc39.x86_64 18/151 Verifying : dwz-0.15-3.fc39.x86_64 19/151 Verifying : ed-1.19-4.fc39.x86_64 20/151 Verifying : efi-srpm-macros-5-9.fc39.noarch 21/151 Verifying : fedora-gpg-keys-39-1.noarch 22/151 Verifying : fedora-repos-39-1.noarch 23/151 Verifying : file-5.44-5.fc39.x86_64 24/151 Verifying : file-libs-5.44-5.fc39.x86_64 25/151 Verifying : filesystem-3.18-6.fc39.x86_64 26/151 Verifying : findutils-1:4.9.0-5.fc39.x86_64 27/151 Verifying : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 28/151 Verifying : fpc-srpm-macros-1.3-8.fc39.noarch 29/151 Verifying : gawk-5.2.2-2.fc39.x86_64 30/151 Verifying : gdbm-libs-1:1.23-4.fc39.x86_64 31/151 Verifying : ghc-srpm-macros-1.6.1-2.fc39.noarch 32/151 Verifying : gmp-1:6.2.1-5.fc39.x86_64 33/151 Verifying : gnat-srpm-macros-6-3.fc39.noarch 34/151 Verifying : grep-3.11-3.fc39.x86_64 35/151 Verifying : gzip-1.12-6.fc39.x86_64 36/151 Verifying : info-7.0.3-3.fc39.x86_64 37/151 Verifying : jansson-2.13.1-7.fc39.x86_64 38/151 Verifying : kernel-srpm-macros-1.0-20.fc39.noarch 39/151 Verifying : keyutils-libs-1.6.1-7.fc39.x86_64 40/151 Verifying : libacl-2.3.1-8.fc39.x86_64 41/151 Verifying : libarchive-3.7.1-1.fc39.x86_64 42/151 Verifying : libattr-2.5.1-8.fc39.x86_64 43/151 Verifying : libblkid-2.39.2-1.fc39.x86_64 44/151 Verifying : libbrotli-1.1.0-1.fc39.x86_64 45/151 Verifying : libcap-ng-0.8.3-8.fc39.x86_64 46/151 Verifying : libcom_err-1.47.0-2.fc39.x86_64 47/151 Verifying : libcurl-8.2.1-3.fc39.x86_64 48/151 Verifying : libdb-5.3.28-56.fc39.x86_64 49/151 Verifying : libeconf-0.5.2-1.fc39.x86_64 50/151 Verifying : libevent-2.1.12-9.fc39.x86_64 51/151 Verifying : libfdisk-2.39.2-1.fc39.x86_64 52/151 Verifying : libffi-3.4.4-4.fc39.x86_64 53/151 Verifying : libidn2-2.3.4-3.fc39.x86_64 54/151 Verifying : libmount-2.39.2-1.fc39.x86_64 55/151 Verifying : libnsl2-2.0.0-6.fc39.x86_64 56/151 Verifying : libpkgconf-1.9.5-2.fc39.x86_64 57/151 Verifying : libpsl-0.21.2-4.fc39.x86_64 58/151 Verifying : libpwquality-1.4.5-6.fc39.x86_64 59/151 Verifying : libselinux-3.5-5.fc39.x86_64 60/151 Verifying : libsemanage-3.5-4.fc39.x86_64 61/151 Verifying : libsepol-3.5-2.fc39.x86_64 62/151 Verifying : libsigsegv-2.14-5.fc39.x86_64 63/151 Verifying : libsmartcols-2.39.2-1.fc39.x86_64 64/151 Verifying : libssh-0.10.5-2.fc39.x86_64 65/151 Verifying : libssh-config-0.10.5-2.fc39.noarch 66/151 Verifying : libtasn1-4.19.0-3.fc39.x86_64 67/151 Verifying : libunistring-1.1-5.fc39.x86_64 68/151 Verifying : libutempter-1.2.1-10.fc39.x86_64 69/151 Verifying : libuuid-2.39.2-1.fc39.x86_64 70/151 Verifying : libverto-0.3.2-6.fc39.x86_64 71/151 Verifying : libxcrypt-4.4.36-2.fc39.x86_64 72/151 Verifying : libxml2-2.10.4-3.fc39.x86_64 73/151 Verifying : libzstd-1.5.5-4.fc39.x86_64 74/151 Verifying : lua-libs-5.4.6-3.fc39.x86_64 75/151 Verifying : lua-srpm-macros-1-9.fc39.noarch 76/151 Verifying : lz4-libs-1.9.4-4.fc39.x86_64 77/151 Verifying : mpfr-4.2.0-3.fc39.x86_64 78/151 Verifying : ncurses-base-6.4-7.20230520.fc39.noarch 79/151 Verifying : ncurses-libs-6.4-7.20230520.fc39.x86_64 80/151 Verifying : ocaml-srpm-macros-8-2.fc39.noarch 81/151 Verifying : openblas-srpm-macros-2-14.fc39.noarch 82/151 Verifying : openldap-2.6.6-1.fc39.x86_64 83/151 Verifying : openssl-libs-1:3.1.1-4.fc39.x86_64 84/151 Verifying : package-notes-srpm-macros-0.5-9.fc39.noarch 85/151 Verifying : patch-2.7.6-22.fc39.x86_64 86/151 Verifying : pcre2-10.42-1.fc39.2.x86_64 87/151 Verifying : pcre2-syntax-10.42-1.fc39.2.noarch 88/151 Verifying : perl-srpm-macros-1-51.fc39.noarch 89/151 Verifying : pkgconf-1.9.5-2.fc39.x86_64 90/151 Verifying : pkgconf-m4-1.9.5-2.fc39.noarch 91/151 Verifying : pkgconf-pkg-config-1.9.5-2.fc39.x86_64 92/151 Verifying : popt-1.19-3.fc39.x86_64 93/151 Verifying : publicsuffix-list-dafsa-20230812-1.fc39.noarch 94/151 Verifying : python-srpm-macros-3.12-4.fc39.noarch 95/151 Verifying : readline-8.2-4.fc39.x86_64 96/151 Verifying : redhat-rpm-config-262-1.fc39.noarch 97/151 Verifying : rpm-4.19.0-1.fc39.x86_64 98/151 Verifying : rpm-build-4.19.0-1.fc39.x86_64 99/151 Verifying : rpm-build-libs-4.19.0-1.fc39.x86_64 100/151 Verifying : rpm-libs-4.19.0-1.fc39.x86_64 101/151 Verifying : rpm-sequoia-1.5.0-1.fc39.x86_64 102/151 Verifying : sed-4.8-14.fc39.x86_64 103/151 Verifying : setup-2.14.4-1.fc39.noarch 104/151 Verifying : sqlite-libs-3.42.0-7.fc39.x86_64 105/151 Verifying : systemd-libs-254.5-2.fc39.x86_64 106/151 Verifying : tar-2:1.35-2.fc39.x86_64 107/151 Verifying : unzip-6.0-62.fc39.x86_64 108/151 Verifying : util-linux-2.39.2-1.fc39.x86_64 109/151 Verifying : util-linux-core-2.39.2-1.fc39.x86_64 110/151 Verifying : which-2.21-40.fc39.x86_64 111/151 Verifying : xxhash-libs-0.8.2-1.fc39.x86_64 112/151 Verifying : xz-5.4.4-1.fc39.x86_64 113/151 Verifying : xz-libs-5.4.4-1.fc39.x86_64 114/151 Verifying : zip-3.0-39.fc39.x86_64 115/151 Verifying : zlib-1.2.13-4.fc39.x86_64 116/151 Verifying : zstd-1.5.5-4.fc39.x86_64 117/151 Verifying : audit-libs-3.1.2-5.fc39.x86_64 118/151 Verifying : bash-5.2.21-1.fc39.x86_64 119/151 Verifying : crypto-policies-20231113-1.gitb402e82.fc39.noarc 120/151 Verifying : elfutils-0.190-1.fc39.x86_64 121/151 Verifying : elfutils-debuginfod-client-0.190-1.fc39.x86_64 122/151 Verifying : elfutils-default-yama-scope-0.190-1.fc39.noarch 123/151 Verifying : elfutils-libelf-0.190-1.fc39.x86_64 124/151 Verifying : elfutils-libs-0.190-1.fc39.x86_64 125/151 Verifying : fedora-release-39-34.noarch 126/151 Verifying : fedora-release-common-39-34.noarch 127/151 Verifying : fedora-release-identity-basic-39-34.noarch 128/151 Verifying : gdb-minimal-13.2-10.fc39.x86_64 129/151 Verifying : glibc-2.38-11.fc39.x86_64 130/151 Verifying : glibc-common-2.38-11.fc39.x86_64 131/151 Verifying : glibc-gconv-extra-2.38-11.fc39.x86_64 132/151 Verifying : glibc-minimal-langpack-2.38-11.fc39.x86_64 133/151 Verifying : go-srpm-macros-3.3.1-1.fc39.noarch 134/151 Verifying : krb5-libs-1.21.2-2.fc39.x86_64 135/151 Verifying : libcap-2.48-8.fc39.x86_64 136/151 Verifying : libgcc-13.2.1-4.fc39.x86_64 137/151 Verifying : libgomp-13.2.1-4.fc39.x86_64 138/151 Verifying : libnghttp2-1.55.1-4.fc39.x86_64 139/151 Verifying : libstdc++-13.2.1-4.fc39.x86_64 140/151 Verifying : libtirpc-1.3.4-0.fc39.x86_64 141/151 Verifying : p11-kit-0.25.3-1.fc39.x86_64 142/151 Verifying : p11-kit-trust-0.25.3-1.fc39.x86_64 143/151 Verifying : pam-1.5.3-3.fc39.x86_64 144/151 Verifying : pam-libs-1.5.3-3.fc39.x86_64 145/151 Verifying : pyproject-srpm-macros-1.10.0-1.fc39.noarch 146/151 Verifying : qt5-srpm-macros-5.15.11-1.fc39.noarch 147/151 Verifying : qt6-srpm-macros-6.6.0-1.fc39.noarch 148/151 Verifying : rpmautospec-rpm-macros-0.3.8-1.fc39.noarch 149/151 Verifying : rust-srpm-macros-25.2-2.fc39.noarch 150/151 Verifying : shadow-utils-2:4.14.0-2.fc39.x86_64 151/151 Installed: alternatives-1.25-1.fc39.x86_64 ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-5.fc39.x86_64 authselect-1.4.3-1.fc39.x86_64 authselect-libs-1.4.3-1.fc39.x86_64 basesystem-11-18.fc39.noarch bash-5.2.21-1.fc39.x86_64 binutils-2.40-13.fc39.x86_64 binutils-gold-2.40-13.fc39.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch coreutils-9.3-4.fc39.x86_64 coreutils-common-9.3-4.fc39.x86_64 cpio-2.14-4.fc39.x86_64 cracklib-2.9.11-2.fc39.x86_64 crypto-policies-20231113-1.gitb402e82.fc39.noarch curl-8.2.1-3.fc39.x86_64 cyrus-sasl-lib-2.1.28-11.fc39.x86_64 debugedit-5.0-10.fc39.x86_64 diffutils-3.10-3.fc39.x86_64 dwz-0.15-3.fc39.x86_64 ed-1.19-4.fc39.x86_64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-1.fc39.x86_64 elfutils-debuginfod-client-0.190-1.fc39.x86_64 elfutils-default-yama-scope-0.190-1.fc39.noarch elfutils-libelf-0.190-1.fc39.x86_64 elfutils-libs-0.190-1.fc39.x86_64 fedora-gpg-keys-39-1.noarch fedora-release-39-34.noarch fedora-release-common-39-34.noarch fedora-release-identity-basic-39-34.noarch fedora-repos-39-1.noarch file-5.44-5.fc39.x86_64 file-libs-5.44-5.fc39.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-1:4.9.0-5.fc39.x86_64 fonts-srpm-macros-1:2.0.5-12.fc39.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.x86_64 gdb-minimal-13.2-10.fc39.x86_64 gdbm-libs-1:1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-2.fc39.noarch glibc-2.38-11.fc39.x86_64 glibc-common-2.38-11.fc39.x86_64 glibc-gconv-extra-2.38-11.fc39.x86_64 glibc-minimal-langpack-2.38-11.fc39.x86_64 gmp-1:6.2.1-5.fc39.x86_64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc39.noarch grep-3.11-3.fc39.x86_64 gzip-1.12-6.fc39.x86_64 info-7.0.3-3.fc39.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.x86_64 krb5-libs-1.21.2-2.fc39.x86_64 libacl-2.3.1-8.fc39.x86_64 libarchive-3.7.1-1.fc39.x86_64 libattr-2.5.1-8.fc39.x86_64 libblkid-2.39.2-1.fc39.x86_64 libbrotli-1.1.0-1.fc39.x86_64 libcap-2.48-8.fc39.x86_64 libcap-ng-0.8.3-8.fc39.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.2.1-3.fc39.x86_64 libdb-5.3.28-56.fc39.x86_64 libeconf-0.5.2-1.fc39.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.2-1.fc39.x86_64 libffi-3.4.4-4.fc39.x86_64 libgcc-13.2.1-4.fc39.x86_64 libgomp-13.2.1-4.fc39.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.2-1.fc39.x86_64 libnghttp2-1.55.1-4.fc39.x86_64 libnsl2-2.0.0-6.fc39.x86_64 libpkgconf-1.9.5-2.fc39.x86_64 libpsl-0.21.2-4.fc39.x86_64 libpwquality-1.4.5-6.fc39.x86_64 libselinux-3.5-5.fc39.x86_64 libsemanage-3.5-4.fc39.x86_64 libsepol-3.5-2.fc39.x86_64 libsigsegv-2.14-5.fc39.x86_64 libsmartcols-2.39.2-1.fc39.x86_64 libssh-0.10.5-2.fc39.x86_64 libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-4.fc39.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-0.fc39.x86_64 libunistring-1.1-5.fc39.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.2-1.fc39.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-2.fc39.x86_64 libxml2-2.10.4-3.fc39.x86_64 libzstd-1.5.5-4.fc39.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.0-3.fc39.x86_64 ncurses-base-6.4-7.20230520.fc39.noarch ncurses-libs-6.4-7.20230520.fc39.x86_64 ocaml-srpm-macros-8-2.fc39.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.x86_64 openssl-libs-1:3.1.1-4.fc39.x86_64 p11-kit-0.25.3-1.fc39.x86_64 p11-kit-trust-0.25.3-1.fc39.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-3.fc39.x86_64 pam-libs-1.5.3-3.fc39.x86_64 patch-2.7.6-22.fc39.x86_64 pcre2-10.42-1.fc39.2.x86_64 pcre2-syntax-10.42-1.fc39.2.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.x86_64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.x86_64 popt-1.19-3.fc39.x86_64 publicsuffix-list-dafsa-20230812-1.fc39.noarch pyproject-srpm-macros-1.10.0-1.fc39.noarch python-srpm-macros-3.12-4.fc39.noarch qt5-srpm-macros-5.15.11-1.fc39.noarch qt6-srpm-macros-6.6.0-1.fc39.noarch readline-8.2-4.fc39.x86_64 redhat-rpm-config-262-1.fc39.noarch rpm-4.19.0-1.fc39.x86_64 rpm-build-4.19.0-1.fc39.x86_64 rpm-build-libs-4.19.0-1.fc39.x86_64 rpm-libs-4.19.0-1.fc39.x86_64 rpm-sequoia-1.5.0-1.fc39.x86_64 rpmautospec-rpm-macros-0.3.8-1.fc39.noarch rust-srpm-macros-25.2-2.fc39.noarch sed-4.8-14.fc39.x86_64 setup-2.14.4-1.fc39.noarch shadow-utils-2:4.14.0-2.fc39.x86_64 sqlite-libs-3.42.0-7.fc39.x86_64 systemd-libs-254.5-2.fc39.x86_64 tar-2:1.35-2.fc39.x86_64 unzip-6.0-62.fc39.x86_64 util-linux-2.39.2-1.fc39.x86_64 util-linux-core-2.39.2-1.fc39.x86_64 which-2.21-40.fc39.x86_64 xxhash-libs-0.8.2-1.fc39.x86_64 xz-5.4.4-1.fc39.x86_64 xz-libs-5.4.4-1.fc39.x86_64 zip-3.0-39.fc39.x86_64 zlib-1.2.13-4.fc39.x86_64 zstd-1.5.5-4.fc39.x86_64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.25-1.fc39.x86_64 ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-5.fc39.x86_64 authselect-1.4.3-1.fc39.x86_64 authselect-libs-1.4.3-1.fc39.x86_64 basesystem-11-18.fc39.noarch bash-5.2.21-1.fc39.x86_64 binutils-2.40-13.fc39.x86_64 binutils-gold-2.40-13.fc39.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.60_v7.0.306-2.fc39.noarch coreutils-9.3-4.fc39.x86_64 coreutils-common-9.3-4.fc39.x86_64 cpio-2.14-4.fc39.x86_64 cracklib-2.9.11-2.fc39.x86_64 crypto-policies-20231113-1.gitb402e82.fc39.noarch curl-8.2.1-3.fc39.x86_64 cyrus-sasl-lib-2.1.28-11.fc39.x86_64 debugedit-5.0-10.fc39.x86_64 diffutils-3.10-3.fc39.x86_64 dwz-0.15-3.fc39.x86_64 ed-1.19-4.fc39.x86_64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-1.fc39.x86_64 elfutils-debuginfod-client-0.190-1.fc39.x86_64 elfutils-default-yama-scope-0.190-1.fc39.noarch elfutils-libelf-0.190-1.fc39.x86_64 elfutils-libs-0.190-1.fc39.x86_64 fedora-gpg-keys-39-1.noarch fedora-release-39-34.noarch fedora-release-common-39-34.noarch fedora-release-identity-basic-39-34.noarch fedora-repos-39-1.noarch file-5.44-5.fc39.x86_64 file-libs-5.44-5.fc39.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-4.9.0-5.fc39.x86_64 fonts-srpm-macros-2.0.5-12.fc39.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.x86_64 gdb-minimal-13.2-10.fc39.x86_64 gdbm-libs-1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-2.fc39.noarch glibc-2.38-11.fc39.x86_64 glibc-common-2.38-11.fc39.x86_64 glibc-gconv-extra-2.38-11.fc39.x86_64 glibc-minimal-langpack-2.38-11.fc39.x86_64 gmp-6.2.1-5.fc39.x86_64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc39.noarch gpg-pubkey-18b8e74c-62f2920f grep-3.11-3.fc39.x86_64 gzip-1.12-6.fc39.x86_64 info-7.0.3-3.fc39.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.x86_64 krb5-libs-1.21.2-2.fc39.x86_64 libacl-2.3.1-8.fc39.x86_64 libarchive-3.7.1-1.fc39.x86_64 libattr-2.5.1-8.fc39.x86_64 libblkid-2.39.2-1.fc39.x86_64 libbrotli-1.1.0-1.fc39.x86_64 libcap-2.48-8.fc39.x86_64 libcap-ng-0.8.3-8.fc39.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.2.1-3.fc39.x86_64 libdb-5.3.28-56.fc39.x86_64 libeconf-0.5.2-1.fc39.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.2-1.fc39.x86_64 libffi-3.4.4-4.fc39.x86_64 libgcc-13.2.1-4.fc39.x86_64 libgomp-13.2.1-4.fc39.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.2-1.fc39.x86_64 libnghttp2-1.55.1-4.fc39.x86_64 libnsl2-2.0.0-6.fc39.x86_64 libpkgconf-1.9.5-2.fc39.x86_64 libpsl-0.21.2-4.fc39.x86_64 libpwquality-1.4.5-6.fc39.x86_64 libselinux-3.5-5.fc39.x86_64 libsemanage-3.5-4.fc39.x86_64 libsepol-3.5-2.fc39.x86_64 libsigsegv-2.14-5.fc39.x86_64 libsmartcols-2.39.2-1.fc39.x86_64 libssh-0.10.5-2.fc39.x86_64 libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-4.fc39.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-0.fc39.x86_64 libunistring-1.1-5.fc39.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.2-1.fc39.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-2.fc39.x86_64 libxml2-2.10.4-3.fc39.x86_64 libzstd-1.5.5-4.fc39.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.0-3.fc39.x86_64 ncurses-base-6.4-7.20230520.fc39.noarch ncurses-libs-6.4-7.20230520.fc39.x86_64 ocaml-srpm-macros-8-2.fc39.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.x86_64 openssl-libs-3.1.1-4.fc39.x86_64 p11-kit-0.25.3-1.fc39.x86_64 p11-kit-trust-0.25.3-1.fc39.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-3.fc39.x86_64 pam-libs-1.5.3-3.fc39.x86_64 patch-2.7.6-22.fc39.x86_64 pcre2-10.42-1.fc39.2.x86_64 pcre2-syntax-10.42-1.fc39.2.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.x86_64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.x86_64 popt-1.19-3.fc39.x86_64 publicsuffix-list-dafsa-20230812-1.fc39.noarch pyproject-srpm-macros-1.10.0-1.fc39.noarch python-srpm-macros-3.12-4.fc39.noarch qt5-srpm-macros-5.15.11-1.fc39.noarch qt6-srpm-macros-6.6.0-1.fc39.noarch readline-8.2-4.fc39.x86_64 redhat-rpm-config-262-1.fc39.noarch rpm-4.19.0-1.fc39.x86_64 rpm-build-4.19.0-1.fc39.x86_64 rpm-build-libs-4.19.0-1.fc39.x86_64 rpm-libs-4.19.0-1.fc39.x86_64 rpm-sequoia-1.5.0-1.fc39.x86_64 rpmautospec-rpm-macros-0.3.8-1.fc39.noarch rust-srpm-macros-25.2-2.fc39.noarch sed-4.8-14.fc39.x86_64 setup-2.14.4-1.fc39.noarch shadow-utils-4.14.0-2.fc39.x86_64 sqlite-libs-3.42.0-7.fc39.x86_64 systemd-libs-254.5-2.fc39.x86_64 tar-1.35-2.fc39.x86_64 unzip-6.0-62.fc39.x86_64 util-linux-2.39.2-1.fc39.x86_64 util-linux-core-2.39.2-1.fc39.x86_64 which-2.21-40.fc39.x86_64 xxhash-libs-0.8.2-1.fc39.x86_64 xz-5.4.4-1.fc39.x86_64 xz-libs-5.4.4-1.fc39.x86_64 zip-3.0-39.fc39.x86_64 zlib-1.2.13-4.fc39.x86_64 zstd-1.5.5-4.fc39.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1701302400 Wrote: /builddir/build/SRPMS/python-pysam-0.22.0-2.fc39.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-x86_64-1701370364.023813/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-x86_64-1701370364.023813/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-x86_64-1701370364.023813/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-rk9y605x/python-pysam/python-pysam.spec) Config(child) 11 minutes 45 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-0.22.0-2.fc39.src.rpm) Config(fedora-39-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1701370364.023813/root. INFO: reusing tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1701370364.023813/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1701370364.023813/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin Finish: chroot init INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.0-1.fc39.x86_64 rpm-sequoia-1.5.0-1.fc39.x86_64 python3-dnf-4.18.1-2.fc39.noarch python3-dnf-plugins-core-4.4.3-1.fc39.noarch yum-4.18.1-2.fc39.noarch Start: build phase for python-pysam-0.22.0-2.fc39.src.rpm Start: build setup for python-pysam-0.22.0-2.fc39.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1701302400 Wrote: /builddir/build/SRPMS/python-pysam-0.22.0-2.fc39.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 25 kB/s | 1.5 kB 00:00 fedora 731 kB/s | 24 kB 00:00 updates 600 kB/s | 21 kB 00:00 Dependencies resolved. ========================================================================================= Package Arch Version Repo Size ========================================================================================= Installing: bzip2-devel x86_64 1.0.8-16.fc39 fedora 214 k gcc x86_64 13.2.1-4.fc39 updates 34 M python3-cython x86_64 3.0.2-1.fc39 fedora 3.8 M python3-devel x86_64 3.12.0-1.fc39 fedora 311 k python3-setuptools noarch 67.7.2-7.fc39 fedora 1.5 M python3-sphinx noarch 1:7.2.6-3.fc39 copr_base 2.5 M python3-sphinx_rtd_theme noarch 1.2.2-1.fc39 fedora 84 k xz-devel x86_64 5.4.4-1.fc39 fedora 66 k zlib-devel x86_64 1.2.13-4.fc39 fedora 45 k Installing dependencies: annobin-docs noarch 12.30-1.fc39 updates 92 k annobin-plugin-gcc x86_64 12.30-1.fc39 updates 959 k cpp x86_64 13.2.1-4.fc39 updates 11 M expat x86_64 2.5.0-3.fc39 fedora 110 k fontawesome4-fonts noarch 1:4.7.0-19.fc39 fedora 204 k fonts-filesystem noarch 1:2.0.5-12.fc39 fedora 8.2 k gc x86_64 8.2.2-4.fc39 fedora 110 k gcc-plugin-annobin x86_64 13.2.1-4.fc39 updates 48 k glibc-devel x86_64 2.38-11.fc39 updates 83 k glibc-headers-x86 noarch 2.38-11.fc39 updates 568 k google-roboto-slab-fonts noarch 1.100263-0.21.20150923git.fc39 fedora 239 k guile22 x86_64 2.2.7-9.fc39 fedora 6.5 M kernel-headers x86_64 6.6.2-201.fc39 updates 1.6 M lato-fonts noarch 2.015-17.fc39 fedora 3.1 M libb2 x86_64 0.98.1-9.fc39 fedora 25 k libmpc x86_64 1.3.1-3.fc39 fedora 70 k libtool-ltdl x86_64 2.4.7-7.fc39 fedora 36 k libxcrypt-devel x86_64 4.4.36-2.fc39 fedora 30 k make x86_64 1:4.4.1-2.fc39 fedora 589 k mpdecimal x86_64 2.5.1-7.fc39 fedora 89 k pyproject-rpm-macros noarch 1.10.0-1.fc39 updates 41 k python-pip-wheel noarch 23.2.1-1.fc39 fedora 1.5 M python-rpm-macros noarch 3.12-4.fc39 fedora 19 k python3 x86_64 3.12.0-1.fc39 fedora 26 k python3-babel noarch 2.12.1-6.fc39 fedora 6.9 M python3-charset-normalizer noarch 3.2.0-2.fc39 fedora 105 k python3-docutils noarch 0.19-5.fc39 fedora 1.0 M python3-idna noarch 3.4-4.fc39 fedora 109 k python3-imagesize noarch 1.4.1-4.fc39 fedora 22 k python3-jinja2 noarch 3.1.2-5.fc39 fedora 506 k python3-libs x86_64 3.12.0-1.fc39 fedora 9.2 M python3-markupsafe x86_64 2.1.3-2.fc39 fedora 30 k python3-packaging noarch 23.1-4.fc39 fedora 114 k python3-pygments noarch 2.15.1-4.fc39 fedora 2.4 M python3-pysocks noarch 1.7.1-20.fc39 fedora 39 k python3-requests noarch 2.28.2-5.fc39 fedora 152 k python3-rpm-generators noarch 14-7.fc39 fedora 30 k python3-rpm-macros noarch 3.12-4.fc39 fedora 14 k python3-snowballstemmer noarch 2.2.0-7.fc39 fedora 257 k python3-sphinx-theme-alabaster noarch 0.7.12-19.fc39 fedora 29 k python3-sphinxcontrib-jquery noarch 4.1-3.fc39 fedora 113 k python3-urllib3 noarch 1.26.18-1.fc39 updates 274 k python3-urllib3+socks noarch 1.26.18-1.fc39 updates 10 k tzdata noarch 2023c-2.fc39 fedora 717 k Transaction Summary ========================================================================================= Install 53 Packages Total download size: 91 M Installed size: 331 M Downloading Packages: (1/53): python3-sphinx-7.2.6-3.fc39.noarch.rpm 27 MB/s | 2.5 MB 00:00 (2/53): expat-2.5.0-3.fc39.x86_64.rpm 274 kB/s | 110 kB 00:00 (3/53): fonts-filesystem-2.0.5-12.fc39.noarch.r 98 kB/s | 8.2 kB 00:00 (4/53): bzip2-devel-1.0.8-16.fc39.x86_64.rpm 436 kB/s | 214 kB 00:00 (5/53): fontawesome4-fonts-4.7.0-19.fc39.noarch 419 kB/s | 204 kB 00:00 (6/53): gc-8.2.2-4.fc39.x86_64.rpm 810 kB/s | 110 kB 00:00 (7/53): google-roboto-slab-fonts-1.100263-0.21. 1.4 MB/s | 239 kB 00:00 (8/53): libb2-0.98.1-9.fc39.x86_64.rpm 310 kB/s | 25 kB 00:00 (9/53): libmpc-1.3.1-3.fc39.x86_64.rpm 862 kB/s | 70 kB 00:00 (10/53): libtool-ltdl-2.4.7-7.fc39.x86_64.rpm 467 kB/s | 36 kB 00:00 (11/53): libxcrypt-devel-4.4.36-2.fc39.x86_64.r 363 kB/s | 30 kB 00:00 (12/53): lato-fonts-2.015-17.fc39.noarch.rpm 7.2 MB/s | 3.1 MB 00:00 (13/53): mpdecimal-2.5.1-7.fc39.x86_64.rpm 1.2 MB/s | 89 kB 00:00 (14/53): make-4.4.1-2.fc39.x86_64.rpm 3.8 MB/s | 589 kB 00:00 (15/53): guile22-2.2.7-9.fc39.x86_64.rpm 12 MB/s | 6.5 MB 00:00 (16/53): python-rpm-macros-3.12-4.fc39.noarch.r 260 kB/s | 19 kB 00:00 (17/53): python3-3.12.0-1.fc39.x86_64.rpm 353 kB/s | 26 kB 00:00 (18/53): python-pip-wheel-23.2.1-1.fc39.noarch. 15 MB/s | 1.5 MB 00:00 (19/53): python3-charset-normalizer-3.2.0-2.fc3 1.4 MB/s | 105 kB 00:00 (20/53): python3-devel-3.12.0-1.fc39.x86_64.rpm 3.9 MB/s | 311 kB 00:00 (21/53): python3-docutils-0.19-5.fc39.noarch.rp 10 MB/s | 1.0 MB 00:00 (22/53): python3-cython-3.0.2-1.fc39.x86_64.rpm 15 MB/s | 3.8 MB 00:00 (23/53): python3-idna-3.4-4.fc39.noarch.rpm 1.4 MB/s | 109 kB 00:00 (24/53): python3-imagesize-1.4.1-4.fc39.noarch. 251 kB/s | 22 kB 00:00 (25/53): python3-babel-2.12.1-6.fc39.noarch.rpm 17 MB/s | 6.9 MB 00:00 (26/53): python3-jinja2-3.1.2-5.fc39.noarch.rpm 6.3 MB/s | 506 kB 00:00 (27/53): python3-markupsafe-2.1.3-2.fc39.x86_64 405 kB/s | 30 kB 00:00 (28/53): python3-packaging-23.1-4.fc39.noarch.r 1.5 MB/s | 114 kB 00:00 (29/53): python3-pysocks-1.7.1-20.fc39.noarch.r 527 kB/s | 39 kB 00:00 (30/53): python3-pygments-2.15.1-4.fc39.noarch. 21 MB/s | 2.4 MB 00:00 (31/53): python3-requests-2.28.2-5.fc39.noarch. 2.0 MB/s | 152 kB 00:00 (32/53): python3-rpm-generators-14-7.fc39.noarc 412 kB/s | 30 kB 00:00 (33/53): python3-libs-3.12.0-1.fc39.x86_64.rpm 31 MB/s | 9.2 MB 00:00 (34/53): python3-rpm-macros-3.12-4.fc39.noarch. 188 kB/s | 14 kB 00:00 (35/53): python3-setuptools-67.7.2-7.fc39.noarc 17 MB/s | 1.5 MB 00:00 (36/53): python3-snowballstemmer-2.2.0-7.fc39.n 2.7 MB/s | 257 kB 00:00 (37/53): python3-sphinx-theme-alabaster-0.7.12- 328 kB/s | 29 kB 00:00 (38/53): python3-sphinx_rtd_theme-1.2.2-1.fc39. 935 kB/s | 84 kB 00:00 (39/53): python3-sphinxcontrib-jquery-4.1-3.fc3 1.1 MB/s | 113 kB 00:00 (40/53): tzdata-2023c-2.fc39.noarch.rpm 8.6 MB/s | 717 kB 00:00 (41/53): zlib-devel-1.2.13-4.fc39.x86_64.rpm 613 kB/s | 45 kB 00:00 (42/53): xz-devel-5.4.4-1.fc39.x86_64.rpm 605 kB/s | 66 kB 00:00 (43/53): annobin-docs-12.30-1.fc39.noarch.rpm 232 kB/s | 92 kB 00:00 (44/53): annobin-plugin-gcc-12.30-1.fc39.x86_64 1.4 MB/s | 959 kB 00:00 (45/53): gcc-plugin-annobin-13.2.1-4.fc39.x86_6 604 kB/s | 48 kB 00:00 (46/53): glibc-devel-2.38-11.fc39.x86_64.rpm 1.0 MB/s | 83 kB 00:00 (47/53): glibc-headers-x86-2.38-11.fc39.noarch. 5.1 MB/s | 568 kB 00:00 (48/53): kernel-headers-6.6.2-201.fc39.x86_64.r 9.3 MB/s | 1.6 MB 00:00 (49/53): cpp-13.2.1-4.fc39.x86_64.rpm 9.8 MB/s | 11 MB 00:01 (50/53): pyproject-rpm-macros-1.10.0-1.fc39.noa 524 kB/s | 41 kB 00:00 (51/53): python3-urllib3+socks-1.26.18-1.fc39.n 122 kB/s | 10 kB 00:00 (52/53): python3-urllib3-1.26.18-1.fc39.noarch. 3.3 MB/s | 274 kB 00:00 (53/53): gcc-13.2.1-4.fc39.x86_64.rpm 26 MB/s | 34 MB 00:01 -------------------------------------------------------------------------------- Total 24 MB/s | 91 MB 00:03 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python-rpm-macros-3.12-4.fc39.noarch 1/53 Installing : fonts-filesystem-1:2.0.5-12.fc39.noarch 2/53 Installing : python3-rpm-macros-3.12-4.fc39.noarch 3/53 Installing : libmpc-1.3.1-3.fc39.x86_64 4/53 Installing : cpp-13.2.1-4.fc39.x86_64 5/53 Installing : pyproject-rpm-macros-1.10.0-1.fc39.noarch 6/53 Installing : fontawesome4-fonts-1:4.7.0-19.fc39.noarch 7/53 Installing : google-roboto-slab-fonts-1.100263-0.21.20150923git 8/53 Installing : lato-fonts-2.015-17.fc39.noarch 9/53 Installing : kernel-headers-6.6.2-201.fc39.x86_64 10/53 Installing : glibc-headers-x86-2.38-11.fc39.noarch 11/53 Installing : glibc-devel-2.38-11.fc39.x86_64 12/53 Installing : libxcrypt-devel-4.4.36-2.fc39.x86_64 13/53 Installing : annobin-docs-12.30-1.fc39.noarch 14/53 Installing : tzdata-2023c-2.fc39.noarch 15/53 Installing : python-pip-wheel-23.2.1-1.fc39.noarch 16/53 Installing : mpdecimal-2.5.1-7.fc39.x86_64 17/53 Installing : libtool-ltdl-2.4.7-7.fc39.x86_64 18/53 Installing : libb2-0.98.1-9.fc39.x86_64 19/53 Installing : gc-8.2.2-4.fc39.x86_64 20/53 Installing : guile22-2.2.7-9.fc39.x86_64 21/53 Installing : make-1:4.4.1-2.fc39.x86_64 22/53 Installing : gcc-13.2.1-4.fc39.x86_64 23/53 Running scriptlet: gcc-13.2.1-4.fc39.x86_64 23/53 Installing : expat-2.5.0-3.fc39.x86_64 24/53 Installing : python3-3.12.0-1.fc39.x86_64 25/53 Installing : python3-libs-3.12.0-1.fc39.x86_64 26/53 Installing : python3-docutils-0.19-5.fc39.noarch 27/53 Installing : python3-idna-3.4-4.fc39.noarch 28/53 Installing : python3-packaging-23.1-4.fc39.noarch 29/53 Installing : python3-rpm-generators-14-7.fc39.noarch 30/53 Installing : python3-babel-2.12.1-6.fc39.noarch 31/53 Installing : python3-charset-normalizer-3.2.0-2.fc39.noarch 32/53 Installing : python3-imagesize-1.4.1-4.fc39.noarch 33/53 Installing : python3-markupsafe-2.1.3-2.fc39.x86_64 34/53 Installing : python3-jinja2-3.1.2-5.fc39.noarch 35/53 Installing : python3-pygments-2.15.1-4.fc39.noarch 36/53 Installing : python3-pysocks-1.7.1-20.fc39.noarch 37/53 Installing : python3-urllib3+socks-1.26.18-1.fc39.noarch 38/53 Installing : python3-urllib3-1.26.18-1.fc39.noarch 39/53 Installing : python3-requests-2.28.2-5.fc39.noarch 40/53 Installing : python3-snowballstemmer-2.2.0-7.fc39.noarch 41/53 Installing : python3-sphinx-theme-alabaster-0.7.12-19.fc39.noar 42/53 Installing : python3-sphinx-1:7.2.6-3.fc39.noarch 43/53 Installing : python3-sphinxcontrib-jquery-4.1-3.fc39.noarch 44/53 Installing : python3-sphinx_rtd_theme-1.2.2-1.fc39.noarch 45/53 Installing : python3-devel-3.12.0-1.fc39.x86_64 46/53 Installing : python3-cython-3.0.2-1.fc39.x86_64 47/53 Installing : python3-setuptools-67.7.2-7.fc39.noarch 48/53 Installing : annobin-plugin-gcc-12.30-1.fc39.x86_64 49/53 Running scriptlet: annobin-plugin-gcc-12.30-1.fc39.x86_64 49/53 Installing : gcc-plugin-annobin-13.2.1-4.fc39.x86_64 50/53 Running scriptlet: gcc-plugin-annobin-13.2.1-4.fc39.x86_64 50/53 Installing : zlib-devel-1.2.13-4.fc39.x86_64 51/53 Installing : xz-devel-5.4.4-1.fc39.x86_64 52/53 Installing : bzip2-devel-1.0.8-16.fc39.x86_64 53/53 Running scriptlet: bzip2-devel-1.0.8-16.fc39.x86_64 53/53 Verifying : python3-sphinx-1:7.2.6-3.fc39.noarch 1/53 Verifying : bzip2-devel-1.0.8-16.fc39.x86_64 2/53 Verifying : expat-2.5.0-3.fc39.x86_64 3/53 Verifying : fontawesome4-fonts-1:4.7.0-19.fc39.noarch 4/53 Verifying : fonts-filesystem-1:2.0.5-12.fc39.noarch 5/53 Verifying : gc-8.2.2-4.fc39.x86_64 6/53 Verifying : google-roboto-slab-fonts-1.100263-0.21.20150923git 7/53 Verifying : guile22-2.2.7-9.fc39.x86_64 8/53 Verifying : lato-fonts-2.015-17.fc39.noarch 9/53 Verifying : libb2-0.98.1-9.fc39.x86_64 10/53 Verifying : libmpc-1.3.1-3.fc39.x86_64 11/53 Verifying : libtool-ltdl-2.4.7-7.fc39.x86_64 12/53 Verifying : libxcrypt-devel-4.4.36-2.fc39.x86_64 13/53 Verifying : make-1:4.4.1-2.fc39.x86_64 14/53 Verifying : mpdecimal-2.5.1-7.fc39.x86_64 15/53 Verifying : python-pip-wheel-23.2.1-1.fc39.noarch 16/53 Verifying : python-rpm-macros-3.12-4.fc39.noarch 17/53 Verifying : python3-3.12.0-1.fc39.x86_64 18/53 Verifying : python3-babel-2.12.1-6.fc39.noarch 19/53 Verifying : python3-charset-normalizer-3.2.0-2.fc39.noarch 20/53 Verifying : python3-cython-3.0.2-1.fc39.x86_64 21/53 Verifying : python3-devel-3.12.0-1.fc39.x86_64 22/53 Verifying : python3-docutils-0.19-5.fc39.noarch 23/53 Verifying : python3-idna-3.4-4.fc39.noarch 24/53 Verifying : python3-imagesize-1.4.1-4.fc39.noarch 25/53 Verifying : python3-jinja2-3.1.2-5.fc39.noarch 26/53 Verifying : python3-libs-3.12.0-1.fc39.x86_64 27/53 Verifying : python3-markupsafe-2.1.3-2.fc39.x86_64 28/53 Verifying : python3-packaging-23.1-4.fc39.noarch 29/53 Verifying : python3-pygments-2.15.1-4.fc39.noarch 30/53 Verifying : python3-pysocks-1.7.1-20.fc39.noarch 31/53 Verifying : python3-requests-2.28.2-5.fc39.noarch 32/53 Verifying : python3-rpm-generators-14-7.fc39.noarch 33/53 Verifying : python3-rpm-macros-3.12-4.fc39.noarch 34/53 Verifying : python3-setuptools-67.7.2-7.fc39.noarch 35/53 Verifying : python3-snowballstemmer-2.2.0-7.fc39.noarch 36/53 Verifying : python3-sphinx-theme-alabaster-0.7.12-19.fc39.noar 37/53 Verifying : python3-sphinx_rtd_theme-1.2.2-1.fc39.noarch 38/53 Verifying : python3-sphinxcontrib-jquery-4.1-3.fc39.noarch 39/53 Verifying : tzdata-2023c-2.fc39.noarch 40/53 Verifying : xz-devel-5.4.4-1.fc39.x86_64 41/53 Verifying : zlib-devel-1.2.13-4.fc39.x86_64 42/53 Verifying : annobin-docs-12.30-1.fc39.noarch 43/53 Verifying : annobin-plugin-gcc-12.30-1.fc39.x86_64 44/53 Verifying : cpp-13.2.1-4.fc39.x86_64 45/53 Verifying : gcc-13.2.1-4.fc39.x86_64 46/53 Verifying : gcc-plugin-annobin-13.2.1-4.fc39.x86_64 47/53 Verifying : glibc-devel-2.38-11.fc39.x86_64 48/53 Verifying : glibc-headers-x86-2.38-11.fc39.noarch 49/53 Verifying : kernel-headers-6.6.2-201.fc39.x86_64 50/53 Verifying : pyproject-rpm-macros-1.10.0-1.fc39.noarch 51/53 Verifying : python3-urllib3+socks-1.26.18-1.fc39.noarch 52/53 Verifying : python3-urllib3-1.26.18-1.fc39.noarch 53/53 Installed: annobin-docs-12.30-1.fc39.noarch annobin-plugin-gcc-12.30-1.fc39.x86_64 bzip2-devel-1.0.8-16.fc39.x86_64 cpp-13.2.1-4.fc39.x86_64 expat-2.5.0-3.fc39.x86_64 fontawesome4-fonts-1:4.7.0-19.fc39.noarch fonts-filesystem-1:2.0.5-12.fc39.noarch gc-8.2.2-4.fc39.x86_64 gcc-13.2.1-4.fc39.x86_64 gcc-plugin-annobin-13.2.1-4.fc39.x86_64 glibc-devel-2.38-11.fc39.x86_64 glibc-headers-x86-2.38-11.fc39.noarch google-roboto-slab-fonts-1.100263-0.21.20150923git.fc39.noarch guile22-2.2.7-9.fc39.x86_64 kernel-headers-6.6.2-201.fc39.x86_64 lato-fonts-2.015-17.fc39.noarch libb2-0.98.1-9.fc39.x86_64 libmpc-1.3.1-3.fc39.x86_64 libtool-ltdl-2.4.7-7.fc39.x86_64 libxcrypt-devel-4.4.36-2.fc39.x86_64 make-1:4.4.1-2.fc39.x86_64 mpdecimal-2.5.1-7.fc39.x86_64 pyproject-rpm-macros-1.10.0-1.fc39.noarch python-pip-wheel-23.2.1-1.fc39.noarch python-rpm-macros-3.12-4.fc39.noarch python3-3.12.0-1.fc39.x86_64 python3-babel-2.12.1-6.fc39.noarch python3-charset-normalizer-3.2.0-2.fc39.noarch python3-cython-3.0.2-1.fc39.x86_64 python3-devel-3.12.0-1.fc39.x86_64 python3-docutils-0.19-5.fc39.noarch python3-idna-3.4-4.fc39.noarch python3-imagesize-1.4.1-4.fc39.noarch python3-jinja2-3.1.2-5.fc39.noarch python3-libs-3.12.0-1.fc39.x86_64 python3-markupsafe-2.1.3-2.fc39.x86_64 python3-packaging-23.1-4.fc39.noarch python3-pygments-2.15.1-4.fc39.noarch python3-pysocks-1.7.1-20.fc39.noarch python3-requests-2.28.2-5.fc39.noarch python3-rpm-generators-14-7.fc39.noarch python3-rpm-macros-3.12-4.fc39.noarch python3-setuptools-67.7.2-7.fc39.noarch python3-snowballstemmer-2.2.0-7.fc39.noarch python3-sphinx-1:7.2.6-3.fc39.noarch python3-sphinx-theme-alabaster-0.7.12-19.fc39.noarch python3-sphinx_rtd_theme-1.2.2-1.fc39.noarch python3-sphinxcontrib-jquery-4.1-3.fc39.noarch python3-urllib3-1.26.18-1.fc39.noarch python3-urllib3+socks-1.26.18-1.fc39.noarch tzdata-2023c-2.fc39.noarch xz-devel-5.4.4-1.fc39.x86_64 zlib-devel-1.2.13-4.fc39.x86_64 Complete! Finish: build setup for python-pysam-0.22.0-2.fc39.src.rpm Start: rpmbuild python-pysam-0.22.0-2.fc39.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1701302400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.CNuU2p + 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 + rm -rf /builddir/build/BUILD/pysam-0.22.0-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/pysam-0.22.0-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/python-pysam-configure-c99.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + rm -rf pysam.egg-info ++ grep -rl '/\* Generated by Cython' + rm pysam/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.gjJH1R + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pysam-0.22.0 + FORCE_CYTHON=1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP' # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=gcc # pysam: (env) CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... no checking for curl_easy_pause in -lcurl... no checking for curl_easy_init in -lcurl... no configure: error: libcurl library not found Support for HTTPS and other SSL-based URLs requires routines from the libcurl library . Building HTSlib with libcurl enabled requires libcurl development files to be installed on the build machine; you may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-libcurl or resolve this error to build HTSlib. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for library containing regcomp... configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: linking htscodecs_bundled.mk to htscodecs.mk # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config HTS_CFLAGS_AVX2=-mavx2 # pysam: htslib_config HTS_CFLAGS_AVX512=-mavx512f # pysam: htslib_config HTS_CFLAGS_SSE4=-msse4.1 -mpopcnt -mssse3 # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running build running build_py creating build creating build/lib.linux-x86_64-cpython-312 creating build/lib.linux-x86_64-cpython-312/pysam copying pysam/config.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/version.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/utils.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/samtools.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/bcftools.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/__init__.py -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/Pileup.py -> build/lib.linux-x86_64-cpython-312/pysam creating build/lib.linux-x86_64-cpython-312/pysam/include copying pysam/include/__init__.py -> build/lib.linux-x86_64-cpython-312/pysam/include running egg_info creating pysam.egg-info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt writing manifest file 'pysam.egg-info/SOURCES.txt' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' warning: no files found matching 'pysam/libc*.c' no previously-included directories found matching 'tests/' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.htslib.cram' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.cram' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.cram' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.cram' to be distributed and are already explicitly excluding 'pysam.include.htslib.cram' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.htslib.htscodecs.htscodecs' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.htscodecs.htscodecs' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.htscodecs.htscodecs' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.htscodecs.htscodecs' to be distributed and are already explicitly excluding 'pysam.include.htslib.htscodecs.htscodecs' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.htslib.m4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.m4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.m4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.m4' to be distributed and are already explicitly excluding 'pysam.include.htslib.m4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.htslib.os' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.htslib.os' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.htslib.os' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.htslib.os' to be distributed and are already explicitly excluding 'pysam.include.htslib.os' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) /usr/lib/python3.12/site-packages/setuptools/command/build_py.py:201: _Warning: Package 'pysam.include.samtools.lz4' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pysam.include.samtools.lz4' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pysam.include.samtools.lz4' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pysam.include.samtools.lz4' to be distributed and are already explicitly excluding 'pysam.include.samtools.lz4' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/csamtools_util.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/htslib_util.c -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/htslib_util.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignedsegment.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignedsegment.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignmentfile.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcalignmentfile.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcf.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcf.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcftools.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbcftools.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbgzf.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcbgzf.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcfaidx.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcfaidx.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libchtslib.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libchtslib.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamfile.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamfile.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamtools.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcsamtools.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabix.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabix.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabix.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabixproxies.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libctabixproxies.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcutils.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcutils.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcutils.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcvcf.pyi -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/libcvcf.pyx -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/py.typed -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/pysam_stream.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/pysam_util.c -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/pysam_util.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/version.h -> build/lib.linux-x86_64-cpython-312/pysam copying pysam/version.pyi -> build/lib.linux-x86_64-cpython-312/pysam creating build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/LICENSE -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/README -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/amplicon_stats.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam2depth.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_addrprg.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_aux.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_cat.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_color.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_consensus.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_fastq.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_flags.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_import.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_index.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_markdup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_mate.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_md.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plcmd.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_quickcheck.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_reheader.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_rmdup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_rmdupse.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_samples.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_sort.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_split.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_stat.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bamshuf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bamtk.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedcov.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedidx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/bedidx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/coverage.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/coverage.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/cram_size.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/cut_target.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/dict.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/dict.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/faidx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/faidx.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/padding.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/padding.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/phase.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/phase.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/reference.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/reference.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/reset.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/reset.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_opts.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_utils.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_view.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sample.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sample.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/sample.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/samtools.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/samtools.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/splaysort.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats_isize.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/tmp_file.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools copying samtools/version.sh -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools creating build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4 copying samtools/config.h -> build/lib.linux-x86_64-cpython-312/pysam/include/samtools creating build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/HMM.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/LICENSE -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/README -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/abuf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bin.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/bin.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/call.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/ccall.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/cols.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/cols.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/consensus.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/convert.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/convert.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/csq.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/dist.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/dist.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/em.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/em.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/extsort.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/filter.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/filter.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/gff.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/gff.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/gff.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/hclust.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/hex.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/kmin.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/main.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/main.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/mcall.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/mpileup.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/mw.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/prob1.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/regidx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/reheader.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/tabix.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfannotate.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfcall.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfcnv.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfconcat.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfconvert.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcffilter.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfhead.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfindex.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfisec.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfmerge.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfnorm.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfplugin.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfquery.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfroh.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfsom.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfsort.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfstats.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfview.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/version.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/version.c.pysam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/version.sh -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools copying bcftools/config.h -> build/lib.linux-x86_64-cpython-312/pysam/include/bcftools creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/LICENSE -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/Makefile -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/README -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/bcf_sr_sort.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/bgzf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/bgzip.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/builddir_vars.mk.in -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/config.h.in -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/config.mk.in -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/configure -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/configure.ac -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/errmod.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/faidx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/header.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/header.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hfile.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hfile_gcs.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hfile_libcurl.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hfile_s3.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hfile_s3_write.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hts.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hts_expr.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hts_os.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/hts_time_funcs.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/htscodecs_bundled.mk -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/htscodecs_external.mk -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/htsfile.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/htslib.mk -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/htslib.pc.in -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/htslib_vars.mk -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/kfunc.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/kstring.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/md5.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/multipart.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/plugin.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/probaln.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/realn.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/regidx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/region.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/sam.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/sam_internal.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/sam_mods.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/synced_bcf_reader.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/tabix.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/tbx.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/textutils.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/thread_pool.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/vcf.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/vcf_sweep.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/vcfutils.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib copying htslib/version.sh -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_codecs.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_codecs.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_decode.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_decode.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_encode.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_encode.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_external.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_index.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_index.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_io.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_io.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_samtools.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_stats.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_stats.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_structs.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/mFILE.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/mFILE.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/misc.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/open_trace_file.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/open_trace_file.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/os.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/string_alloc.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram copying htslib/cram/string_alloc.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_check_compile_flags_needed.m4 -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/pkg.m4 -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4 creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/os copying htslib/os/lzma_stub.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/os copying htslib/os/rand.c -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/os copying htslib/config.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib creating build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_expr.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kroundup.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib running build_ext creating htslib/config_vars.h for 'pysam.libchtslib' extension building 'libhts.a' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kfunc.o kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kstring.o kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bgzf.o bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o errmod.o errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o faidx.o faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o header.o header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.18"' > version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts.o hts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_expr.o hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_os.o hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o md5.o md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o multipart.o multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o probaln.o probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o realn.o realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o region.o region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o sam.o sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o sam_mods.o sam_mods.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o tbx.o tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o textutils.o textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o thread_pool.o thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf.o vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcfutils.o vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_decode.o cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_io.o cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -mavx2 -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -mavx512f -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -msse4.1 -mpopcnt -mssse3 -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o ranlib libhts.a Compiling pysam/libchtslib.pyx because it changed. [1/1] Cythonizing pysam/libchtslib.pyx building 'pysam.libchtslib' extension creating build/temp.linux-x86_64-cpython-312 creating build/temp.linux-x86_64-cpython-312/pysam gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/htslib_util.c -o build/temp.linux-x86_64-cpython-312/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/libchtslib.c -o build/temp.linux-x86_64-cpython-312/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/htslib_util.o build/temp.linux-x86_64-cpython-312/pysam/libchtslib.o htslib/kfunc.o htslib/kstring.o htslib/bcf_sr_sort.o htslib/bgzf.o htslib/errmod.o htslib/faidx.o htslib/header.o htslib/hfile.o htslib/hts.o htslib/hts_expr.o htslib/hts_os.o htslib/md5.o htslib/multipart.o htslib/probaln.o htslib/realn.o htslib/regidx.o htslib/region.o htslib/sam.o htslib/sam_mods.o htslib/synced_bcf_reader.o htslib/vcf_sweep.o htslib/tbx.o htslib/textutils.o htslib/thread_pool.o htslib/vcf.o htslib/vcfutils.o htslib/cram/cram_codecs.o htslib/cram/cram_decode.o htslib/cram/cram_encode.o htslib/cram/cram_external.o htslib/cram/cram_index.o htslib/cram/cram_io.o htslib/cram/cram_stats.o htslib/cram/mFILE.o htslib/cram/open_trace_file.o htslib/cram/pooled_alloc.o htslib/cram/string_alloc.o htslib/htscodecs/htscodecs/arith_dynamic.o htslib/htscodecs/htscodecs/fqzcomp_qual.o htslib/htscodecs/htscodecs/htscodecs.o htslib/htscodecs/htscodecs/pack.o htslib/htscodecs/htscodecs/rANS_static4x16pr.o htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.o htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.o htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.o htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.o htslib/htscodecs/htscodecs/rANS_static32x16pr.o htslib/htscodecs/htscodecs/rANS_static.o htslib/htscodecs/htscodecs/rle.o htslib/htscodecs/htscodecs/tokenise_name3.o htslib/htscodecs/htscodecs/utils.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -o build/lib.linux-x86_64-cpython-312/pysam/libchtslib.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension Compiling pysam/libcsamtools.pyx because it changed. [1/1] Cythonizing pysam/libcsamtools.pyx building 'pysam.libcsamtools' extension creating build/temp.linux-x86_64-cpython-312/samtools creating build/temp.linux-x86_64-cpython-312/samtools/lz4 gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/libcsamtools.c -o build/temp.linux-x86_64-cpython-312/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_color.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_import.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_index.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_md.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra.0’: samtools/bam_sort.c.pysam.c:2986:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2986 | seq[j] = comp[tmp]; | ~~~~~~~^~~~~~~~~~~ samtools/bam_sort.c.pysam.c:2973:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000 2973 | char seq_[10000], *seq = seq_; | ^~~~ gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_split.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bamtk.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bedcov.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/bedidx.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/coverage.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/cram_size.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/cut_target.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/dict.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/faidx.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/lz4/lz4.c -o build/temp.linux-x86_64-cpython-312/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/padding.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/phase.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/reference.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/reset.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/sam_view.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/sample.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/samtools.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/stats.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-x86_64-cpython-312/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcsamtools.o build/temp.linux-x86_64-cpython-312/samtools/amplicon_stats.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_consensus.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_fastq.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_import.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_samples.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/consensus_pileup.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/coverage.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/cram_size.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/dict.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/faidx.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/lz4/lz4.o build/temp.linux-x86_64-cpython-312/samtools/padding.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/phase.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/reference.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/reset.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/sample.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/samtools.pysam.o build/temp.linux-x86_64-cpython-312/samtools/stats.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-cpython-312/samtools/tmp_file.c.pysam.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcsamtools.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN samtools/bam_sort.c.pysam.c: In function ‘reverse_complement.isra’: samtools/bam_sort.c.pysam.c:2986:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 2986 | seq[j] = comp[tmp]; | ^ samtools/bam_sort.c.pysam.c:2973:10: note: at offset 2147483647 into destination object ‘seq_’ of size 10000 2973 | char seq_[10000], *seq = seq_; | ^ Compiling pysam/libcbcftools.pyx because it changed. [1/1] Cythonizing pysam/libcbcftools.pyx building 'pysam.libcbcftools' extension creating build/temp.linux-x86_64-cpython-312/bcftools gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/HMM.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/abuf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/bcftools.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/bin.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/ccall.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/cols.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/consensus.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/convert.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/csq.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/dist.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/em.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/extsort.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/filter.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/gff.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/gff.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/hclust.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/kmin.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/main.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/mcall.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/prob1.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/read_consensus.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/regidx.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/reheader.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/tabix.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:860:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 860 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pysam-0.22.0/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:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c bcftools/version.c.pysam.c -o build/temp.linux-x86_64-cpython-312/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/libcbcftools.c -o build/temp.linux-x86_64-cpython-312/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/abuf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bcftools.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/bin.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/cols.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/convert.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/csq.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/dist.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/em.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/extsort.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/filter.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/gff.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/gvcf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/hclust.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/kmin.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/main.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/mcall.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/mpileup.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/ploidy.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/prob1.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/read_consensus.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/regidx.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/reheader.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/smpl_ilist.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/str_finder.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/tabix.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/tsv2vcf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfannotate.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfbuf.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfcall.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfcnv.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfconcat.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfconvert.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcffilter.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfhead.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfindex.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfisec.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfmerge.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfnorm.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfplugin.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfquery.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfroh.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfsom.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfsort.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfstats.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcfview.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/vcmp.c.pysam.o build/temp.linux-x86_64-cpython-312/bcftools/version.c.pysam.o build/temp.linux-x86_64-cpython-312/pysam/libcbcftools.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcbcftools.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:860:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 860 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^ /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^ Compiling pysam/libcutils.pyx because it changed. [1/1] Cythonizing pysam/libcutils.pyx building 'pysam.libcutils' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/libcutils.c -o build/temp.linux-x86_64-cpython-312/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/pysam_util.c -o build/temp.linux-x86_64-cpython-312/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcutils.o build/temp.linux-x86_64-cpython-312/pysam/pysam_util.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcsamtools.cpython-312-x86_64-linux-gnu -lcbcftools.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcutils.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcalignmentfile.pyx: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 Compiling pysam/libcalignmentfile.pyx because it changed. [1/1] Cythonizing pysam/libcalignmentfile.pyx building 'pysam.libcalignmentfile' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/libcalignmentfile.c -o build/temp.linux-x86_64-cpython-312/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:20430:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 20430 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:37151:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37151 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcalignmentfile.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcalignmentfile.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcsamfile.pyx because it changed. [1/1] Cythonizing pysam/libcsamfile.pyx building 'pysam.libcsamfile' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/libcsamfile.c -o build/temp.linux-x86_64-cpython-312/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcsamfile.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcsamfile.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcalignedsegment.pyx:760:14: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. warning: pysam/libcalignedsegment.pyx:760:32: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. Compiling pysam/libcalignedsegment.pyx because it changed. [1/1] Cythonizing pysam/libcalignedsegment.pyx building 'pysam.libcalignedsegment' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/libcalignedsegment.c -o build/temp.linux-x86_64-cpython-312/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcalignedsegment.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcalignedsegment.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabix.pyx because it changed. [1/1] Cythonizing pysam/libctabix.pyx building 'pysam.libctabix' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/libctabix.c -o build/temp.linux-x86_64-cpython-312/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libctabix.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libctabix.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcfaidx.pyx because it changed. [1/1] Cythonizing pysam/libcfaidx.pyx building 'pysam.libcfaidx' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/libcfaidx.c -o build/temp.linux-x86_64-cpython-312/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcfaidx.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcfaidx.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcf.pyx because it changed. [1/1] Cythonizing pysam/libcbcf.pyx building 'pysam.libcbcf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/libcbcf.c -o build/temp.linux-x86_64-cpython-312/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’: pysam/libcbcf.c:86755:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 86755 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’: pysam/libcbcf.c:81419:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81419 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’: pysam/libcbcf.c:44519:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44519 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:44545:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44545 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’: pysam/libcbcf.c:81103:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81103 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcbcf.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcbcf.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbgzf.pyx because it changed. [1/1] Cythonizing pysam/libcbgzf.pyx building 'pysam.libcbgzf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/libcbgzf.c -o build/temp.linux-x86_64-cpython-312/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcbgzf.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcbgzf.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libctabixproxies.pyx because it changed. [1/1] Cythonizing pysam/libctabixproxies.pyx building 'pysam.libctabixproxies' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/libctabixproxies.c -o build/temp.linux-x86_64-cpython-312/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libctabixproxies.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libctabixproxies.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN warning: pysam/libcvcf.pyx:1083:27: Unreachable code Compiling pysam/libcvcf.pyx because it changed. [1/1] Cythonizing pysam/libcvcf.pyx building 'pysam.libcvcf' extension gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/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/python3.12 -c pysam/libcvcf.c -o build/temp.linux-x86_64-cpython-312/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.0’: pysam/libcvcf.c:29574:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 29574 | __pyx_t_11 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:24723:10: note: ‘__pyx_v_qual’ was declared here 24723 | double __pyx_v_qual; | ^~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC build/temp.linux-x86_64-cpython-312/pysam/libcvcf.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -Lbuild/lib.linux-x86_64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-x86_64-linux-gnu -lcutils.cpython-312-x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pysam/libcvcf.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN ++ echo /builddir/build/BUILD/pysam-0.22.0/build/lib.linux-x86_64-cpython-312 + PYTHONPATH=/builddir/build/BUILD/pysam-0.22.0/build/lib.linux-x86_64-cpython-312 + sphinx-build-3 doc html Running Sphinx v7.2.6 making output directory... done [autosummary] generating autosummary for: api.rst, benchmarking.rst, developer.rst, faq.rst, glossary.rst, index.rst, installation.rst, release.rst, usage.rst loading intersphinx inventory from https://docs.python.org/3.12/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3.12/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3.12/objects.inv (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution')) building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 9 source files that are out of date updating environment: [new config] 9 added, 0 changed, 0 removed reading sources... [100%] usage looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done copying assets... copying static files... done copying extra files... done done writing output... [100%] usage generating indices... genindex done writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 1 warning. The HTML pages are in html. + rm -rf html/.doctrees html/.buildinfo + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.IJBKCl + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64 ++ dirname /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pysam-0.22.0 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + /usr/bin/python3 setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64 --prefix /usr # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=gcc # pysam: (env) CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... no checking for curl_easy_pause in -lcurl... no checking for curl_easy_init in -lcurl... no configure: error: libcurl library not found Support for HTTPS and other SSL-based URLs requires routines from the libcurl library . Building HTSlib with libcurl enabled requires libcurl development files to be installed on the build machine; you may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-libcurl or resolve this error to build HTSlib. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking how to run the C preprocessor... gcc -E checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking whether _XOPEN_SOURCE is declared... no checking C compiler flags needed for ssse3... -mssse3 checking C compiler flags needed for popcnt... -mpopcnt checking C compiler flags needed for sse4.1... -msse4.1 checking C compiler flags needed for avx2... -mavx2 checking C compiler flags needed for avx512f... -mavx512f checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the linker supports versioned symbols... no checking whether the compiler accepts -fvisibility=hidden... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h config.status: config.h is unchanged config.status: linking htscodecs_bundled.mk to htscodecs.mk # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config HTS_CFLAGS_AVX2=-mavx2 # pysam: htslib_config HTS_CFLAGS_AVX512=-mavx512f # pysam: htslib_config HTS_CFLAGS_SSE4=-msse4.1 -mpopcnt -mssse3 # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running install /usr/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer, pypa/build or other standards-based tools. Follow the current Python packaging guidelines when building Python RPM packages. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html and https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ for details. ******************************************************************************** !! self.initialize_options() running install_lib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64 creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12 creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/__pycache__/version.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/__pycache__/config.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/__pycache__/samtools.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/__pycache__/Pileup.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/__pycache__/utils.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/__pycache__/__init__.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-cpython-312/pysam/libcvcf.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabixproxies.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbgzf.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcf.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcfaidx.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabix.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignedsegment.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamfile.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignmentfile.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcutils.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcftools.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamtools.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libchtslib.cpython-312-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/version.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/version.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/pysam_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/pysam_util.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/pysam_stream.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/py.typed -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcvcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcvcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcvcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcutils.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcutils.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcutils.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabixproxies.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabixproxies.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabixproxies.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabix.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabix.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libctabix.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamtools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamtools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamtools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcsamfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libchtslib.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libchtslib.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libchtslib.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcfaidx.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcfaidx.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcfaidx.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbgzf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbgzf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcftools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcftools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcftools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcbcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignmentfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignmentfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignmentfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignedsegment.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignedsegment.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/libcalignedsegment.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/htslib_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/htslib_util.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/csamtools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/cbcftools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/vcfutils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/vcf_sweep.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/thread_pool.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/tbx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/synced_bcf_reader.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/sam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/kstring.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/ksort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/kseq.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/kroundup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/knetfile.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/klist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/khash_str2int.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/khash.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/kfunc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/kbitset.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hts_os.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hts_log.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hts_expr.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hts_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hts_defs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hts.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/hfile.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/faidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib/bgzf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/os/rand.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/os/lzma_stub.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4/pkg.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4/hts_prog_cc_warnings.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4/hts_hide_dynamic_syms.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/m4/hts_check_compile_flags_needed.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/version.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/varint2.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/varint.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/utils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/utils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rle.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rle.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_word.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/permute.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pack.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pack.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/string_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/string_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/pooled_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/os.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/open_trace_file.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/open_trace_file.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/misc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/mFILE.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/mFILE.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_structs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_stats.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_io.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_io.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_index.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_index.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_external.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_encode.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_encode.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_decode.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_decode.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_codecs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram_codecs.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/cram/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/vcfutils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/vcf_sweep.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/thread_pool_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/thread_pool.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/textutils_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/textutils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/tbx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/synced_bcf_reader.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/sam_mods.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/sam_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/sam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/region.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/realn.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/probaln.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/plugin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/multipart.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/md5.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/kstring.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/kfunc.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib_vars.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib.pc.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htslib.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htsfile.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs_external.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/htscodecs_bundled.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hts_time_funcs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hts_os.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hts_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hts_expr.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hts.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hfile_s3_write.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hfile_s3.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hfile_libcurl.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hfile_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hfile_gcs.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/hfile.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/header.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/header.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/errmod.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/configure.ac -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/configure -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/config.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/config.h.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/builddir_vars.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/bgzip.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/bgzf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/bcf_sr_sort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/bcf_sr_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/README -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/Makefile -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-cpython-312/pysam/include/htslib/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/version.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/version.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcmp.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcmp.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcmp.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfview.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfview.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfstats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfstats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfsort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfsom.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfsom.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfroh.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfroh.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfquery.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfquery.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfplugin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfplugin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfnorm.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfnorm.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfmerge.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfmerge.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfisec.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfisec.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfindex.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfindex.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfhead.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfhead.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfgtcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcffilter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcffilter.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfconvert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfconvert.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfconcat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfconcat.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfcnv.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfcnv.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfcall.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfannotate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/vcfannotate.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/variantkey.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/utlist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/tsv2vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/tsv2vcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/tsv2vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/tabix.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/str_finder.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/str_finder.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/str_finder.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/smpl_ilist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/smpl_ilist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/smpl_ilist.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/regidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/read_consensus.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/read_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/read_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/rbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/prob1.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/prob1.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/prob1.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/ploidy.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/ploidy.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/ploidy.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/mw.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/mpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/mpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/mcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/mcall.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/main.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/main.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/kmin.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/kmin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/kmin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/kheap.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/khash_str2str.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/hex.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/hclust.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/hclust.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/hclust.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/gvcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/gvcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/gvcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/gff.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/gff.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/gff.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/filter.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/filter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/filter.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/extsort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/extsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/extsort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/em.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/em.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/dist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/dist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/dist.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/dbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/csq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/csq.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/convert.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/convert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/convert.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/cols.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/cols.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/cols.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/cigar_state.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/ccall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/ccall.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/call.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bin.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bcftools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bcftools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bcftools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam_sample.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam_sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam_sample.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf_indel.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf_iaux.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/bam2bcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/abuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/abuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/abuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/README -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/HMM.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/HMM.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-cpython-312/pysam/include/bcftools/HMM.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/bcftools creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4/lz4.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4/lz4.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4/lz4.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/lz4/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/tmp_file.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/tmp_file.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/tmp_file.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/stats_isize.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/stats_isize.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/stats_isize.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/stats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/splaysort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/samtools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/samtools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sample.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sample.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_view.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_view.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_utils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_utils.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_utils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_opts.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_opts.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/sam_opts.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/reset.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/reset.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/reference.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/reference.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/phase.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/phase.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/padding.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/padding.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/faidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/dict.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/dict.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/cut_target.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/cut_target.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/cram_size.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/cram_size.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/coverage.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/coverage.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/consensus_pileup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/consensus_pileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/consensus_pileup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bedidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bedidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bedidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bedcov.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bedcov.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bamtk.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bamtk.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bamshuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bamshuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_stat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_stat.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_split.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_split.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_sort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_samples.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_samples.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_rmdupse.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_rmdupse.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_rmdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_rmdup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_quickcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_quickcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_plcmd.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_plcmd.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_plbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_plbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_plbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_md.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_md.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_mate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_mate.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_markdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_markdup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_lpileup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_lpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_lpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_index.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_index.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_import.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_import.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_flags.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_flags.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_fastq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_fastq.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_color.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_color.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_cat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_cat.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_aux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_aux.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_ampliconclip.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_ampliconclip.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_addrprg.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam_addrprg.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam2depth.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam2depth.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/bam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/amplicon_stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/amplicon_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/README -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/samtools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-cpython-312/pysam/include/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include copying build/lib.linux-x86_64-cpython-312/pysam/Pileup.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/bcftools.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/samtools.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/utils.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/version.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-x86_64-cpython-312/pysam/config.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam byte-compiling /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/include/__init__.py to __init__.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/bcftools.py to bcftools.cpython-312.pyc writing byte-compilation script '/tmp/tmpzwo7i7t5.py' /usr/bin/python3 /tmp/tmpzwo7i7t5.py removing /tmp/tmpzwo7i7t5.py running install_egg_info running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam-0.22.0-py3.12.egg-info running install_scripts + rm -rfv /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/bin/__pycache__ + rm /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcalignedsegment.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcalignmentfile.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcbcf.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcbcftools.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcbgzf.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcfaidx.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libchtslib.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcsamfile.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcsamtools.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libctabix.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libctabixproxies.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcutils.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/libcvcf.pyx + rm /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/htslib_util.c /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12/site-packages/pysam/pysam_util.c + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 0.22.0-2.fc39 --unique-debug-suffix -0.22.0-2.fc39.x86_64 --unique-debug-src-base python-pysam-0.22.0-2.fc39.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/pysam-0.22.0 find-debuginfo: starting Extracting debug info from 13 files DWARF-compressing 13 files sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/python-pysam-0.22.0-2.fc39.x86_64 53749 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/samtools/version.sh from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/bcftools/version.sh from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/htslib/configure from /bin/sh to #!/usr/bin/sh mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/htslib/version.sh from /bin/sh to #!/usr/bin/sh + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib/debug/usr/lib64/python3.12 using python3.12 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/lib64/python3.12 using python3.12 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: python3-pysam-0.22.0-2.fc39.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.q104Nk + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/share/doc/python3-pysam + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/share/doc/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/README.rst /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/share/doc/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.Xa2CxI + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + LICENSEDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/share/licenses/python3-pysam + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/COPYING /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/bcftools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/htslib/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/samtools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/share/licenses/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 warning: File listed twice: /usr/share/licenses/python3-pysam/LICENSE warning: File listed twice: /usr/share/licenses/python3-pysam/LICENSE Provides: bundled(bcftools) = 1.18 bundled(htslib) = 1.18 bundled(samtools) = 1.18 libcalignedsegment.cpython-312-x86_64-linux-gnu.so()(64bit) libcalignmentfile.cpython-312-x86_64-linux-gnu.so()(64bit) libcbcf.cpython-312-x86_64-linux-gnu.so()(64bit) libcbcftools.cpython-312-x86_64-linux-gnu.so()(64bit) libcbgzf.cpython-312-x86_64-linux-gnu.so()(64bit) libcfaidx.cpython-312-x86_64-linux-gnu.so()(64bit) libchtslib.cpython-312-x86_64-linux-gnu.so()(64bit) libcsamfile.cpython-312-x86_64-linux-gnu.so()(64bit) libcsamtools.cpython-312-x86_64-linux-gnu.so()(64bit) libctabix.cpython-312-x86_64-linux-gnu.so()(64bit) libctabixproxies.cpython-312-x86_64-linux-gnu.so()(64bit) libcutils.cpython-312-x86_64-linux-gnu.so()(64bit) libcvcf.cpython-312-x86_64-linux-gnu.so()(64bit) python-pysam = 0.22.0-2.fc39 python3-pysam = 0.22.0-2.fc39 python3-pysam(x86-64) = 0.22.0-2.fc39 python3.12-pysam = 0.22.0-2.fc39 python3.12dist(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_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libcbcftools.cpython-312-x86_64-linux-gnu.so()(64bit) libchtslib.cpython-312-x86_64-linux-gnu.so()(64bit) libcsamtools.cpython-312-x86_64-linux-gnu.so()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) python(abi) = 3.12 rtld(GNU_HASH) Obsoletes: python-pysam < 0.22.0-2.fc39 Processing files: python3-pysam-devel-0.22.0-2.fc39.x86_64 Provides: python-pysam-devel = 0.22.0-2.fc39 python3-pysam-devel = 0.22.0-2.fc39 python3-pysam-devel(x86-64) = 0.22.0-2.fc39 python3.12-pysam-devel = 0.22.0-2.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/sh python(abi) = 3.12 Processing files: python-pysam-doc-0.22.0-2.fc39.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.MXGW7R + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/share/doc/python-pysam-doc + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/share/doc/python-pysam-doc + cp -pr /builddir/build/BUILD/pysam-0.22.0/html /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64/usr/share/doc/python-pysam-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-pysam-doc = 0.22.0-2.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-pysam-debugsource-0.22.0-2.fc39.x86_64 Provides: python-pysam-debugsource = 0.22.0-2.fc39 python-pysam-debugsource(x86-64) = 0.22.0-2.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-pysam-debuginfo-0.22.0-2.fc39.x86_64 Provides: debuginfo(build-id) = 0035c92c740d5b1ca22543f89ab7bd60d616e882 debuginfo(build-id) = 1b7fb802c5113819a7da5d2e0f57dfb9463e33f8 debuginfo(build-id) = 279361485153014a86f3df25ee722bd887814b0f debuginfo(build-id) = 30e12500b529ed20fd08eb004189fbf5dbe513e4 debuginfo(build-id) = 373255a3f6b7c3ebabdc20595418d75c139dc7f7 debuginfo(build-id) = 516698d5b75f0a464592ad2a004133e4fade3866 debuginfo(build-id) = 6dc5ede8bad556070bdbae33a4f2306b016df7dc debuginfo(build-id) = 74a0cc1933fe99aaf611721503eb9407e42cf0dc debuginfo(build-id) = ad8b574e4b65bb3d2c7932232bfbbc64a92c87c6 debuginfo(build-id) = ba2e78bdea94305b5fdc8ebe7aef440e9a4cb8cb debuginfo(build-id) = c1e96f271baba3493770ed57f98c195c4942f958 debuginfo(build-id) = ced3be35aeaead4508d5c80599f349c5afb688c8 debuginfo(build-id) = f6061a0899ad0895cd626035cf89cc3333734f9b libcalignedsegment.cpython-312-x86_64-linux-gnu.so-0.22.0-2.fc39.x86_64.debug()(64bit) libcalignmentfile.cpython-312-x86_64-linux-gnu.so-0.22.0-2.fc39.x86_64.debug()(64bit) libcbcf.cpython-312-x86_64-linux-gnu.so-0.22.0-2.fc39.x86_64.debug()(64bit) libcbcftools.cpython-312-x86_64-linux-gnu.so-0.22.0-2.fc39.x86_64.debug()(64bit) libcbgzf.cpython-312-x86_64-linux-gnu.so-0.22.0-2.fc39.x86_64.debug()(64bit) libcfaidx.cpython-312-x86_64-linux-gnu.so-0.22.0-2.fc39.x86_64.debug()(64bit) libchtslib.cpython-312-x86_64-linux-gnu.so-0.22.0-2.fc39.x86_64.debug()(64bit) libcsamfile.cpython-312-x86_64-linux-gnu.so-0.22.0-2.fc39.x86_64.debug()(64bit) libcsamtools.cpython-312-x86_64-linux-gnu.so-0.22.0-2.fc39.x86_64.debug()(64bit) libctabix.cpython-312-x86_64-linux-gnu.so-0.22.0-2.fc39.x86_64.debug()(64bit) libctabixproxies.cpython-312-x86_64-linux-gnu.so-0.22.0-2.fc39.x86_64.debug()(64bit) libcutils.cpython-312-x86_64-linux-gnu.so-0.22.0-2.fc39.x86_64.debug()(64bit) libcvcf.cpython-312-x86_64-linux-gnu.so-0.22.0-2.fc39.x86_64.debug()(64bit) python-pysam-debuginfo = 0.22.0-2.fc39 python3-pysam-debuginfo = 0.22.0-2.fc39 python3-pysam-debuginfo(x86-64) = 0.22.0-2.fc39 python3.12-pysam-debuginfo = 0.22.0-2.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-pysam-debugsource(x86-64) = 0.22.0-2.fc39 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64 Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.22.0-2.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.22.0-2.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/python3-pysam-devel-0.22.0-2.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/python3-pysam-0.22.0-2.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/python-pysam-doc-0.22.0-2.fc39.noarch.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.fysLcG + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc39.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.Odhi2X + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/pysam-0.22.0-SPECPARTS + 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-0.22.0-2.fc39.src.rpm Finish: build phase for python-pysam-0.22.0-2.fc39.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-x86_64-1701370364.023813/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-x86_64-1701370364.023813/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-x86_64-1701370364.023813/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/python-pysam-0.22.0-2.fc39.src.rpm) Config(child) 6 minutes 34 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "python3-pysam-devel", "epoch": null, "version": "0.22.0", "release": "2.fc39", "arch": "x86_64" }, { "name": "python-pysam-debugsource", "epoch": null, "version": "0.22.0", "release": "2.fc39", "arch": "x86_64" }, { "name": "python3-pysam", "epoch": null, "version": "0.22.0", "release": "2.fc39", "arch": "x86_64" }, { "name": "python-pysam", "epoch": null, "version": "0.22.0", "release": "2.fc39", "arch": "src" }, { "name": "python-pysam-doc", "epoch": null, "version": "0.22.0", "release": "2.fc39", "arch": "noarch" }, { "name": "python3-pysam-debuginfo", "epoch": null, "version": "0.22.0", "release": "2.fc39", "arch": "x86_64" } ] } RPMResults finished