Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c116' (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/7040459-epel-8-x86_64 --chroot epel-8-x86_64 Version: 0.70 PID: 6547 Logging PID: 6548 Task: {'appstream': False, 'background': False, 'bootstrap': 'off', 'build_id': 7040459, 'buildroot_pkgs': [], 'chroot': 'epel-8-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '7c32cbdc9bb761611c35d7d024bc41f5b258c3dd', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/aminasyan/el8-collection/python-pysam', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'python-pysam', 'package_version': '0.22.0-1', 'project_dirname': 'el8-collection', 'project_name': 'el8-collection', 'project_owner': 'aminasyan', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/aminasyan/el8-collection/epel-8-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}, {'baseurl': 'https://copr-be.cloud.fedoraproject.org/results/aminasyan/el8-collection/epel-8-x86_64/', 'id': 'https_copr_be_cloud_fedoraproject_org_results_aminasyan_el8_collection_chroot', 'name': 'Additional repo https_copr_be_cloud_fedoraproject_org_results_aminasyan_el8_collection_chroot'}], 'sandbox': 'aminasyan/el8-collection--aminasyan', 'source_json': {}, 'source_type': None, 'submitter': 'aminasyan', 'tags': [], 'task_id': '7040459-epel-8-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/aminasyan/el8-collection/python-pysam /var/lib/copr-rpmbuild/workspace/workdir-wwvwxr5d/python-pysam --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/aminasyan/el8-collection/python-pysam', '/var/lib/copr-rpmbuild/workspace/workdir-wwvwxr5d/python-pysam', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-wwvwxr5d/python-pysam'... Running: git checkout 7c32cbdc9bb761611c35d7d024bc41f5b258c3dd -- cmd: ['git', 'checkout', '7c32cbdc9bb761611c35d7d024bc41f5b258c3dd', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-wwvwxr5d/python-pysam rc: 0 stdout: stderr: Note: switching to '7c32cbdc9bb761611c35d7d024bc41f5b258c3dd'. 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 7c32cbd automatic import of python-pysam Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-wwvwxr5d/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/aminasyan/el8-collection/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 29.6M 0 --:--:-- --:--:-- --:--:-- 29.8M /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-wwvwxr5d/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-wwvwxr5d/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1708464790.174803 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.5 starting (python version = 3.12.1, NVR = mock-5.5-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-wwvwxr5d/python-pysam/python-pysam.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-wwvwxr5d/python-pysam --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1708464790.174803 -r /var/lib/copr-rpmbuild/results/configs/child.cfg 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-wwvwxr5d/python-pysam/python-pysam.spec) Config(rhel+epel-8-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.5 INFO: Mock Version: 5.5 Start: chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-8-x86_64-1708464790.174803/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 (fallback) INFO: Buildroot is handled by package management from host and used with --installroot: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.18.2-1.fc39.noarch python3-dnf-plugins-core-4.4.4-1.fc39.noarch yum-4.18.2-1.fc39.noarch dnf5-5.1.12-1.fc39.x86_64 dnf5-plugins-5.1.12-1.fc39.x86_64 Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 4.4 MB/s | 937 kB 00:00 Additional repo https_copr_be_cloud_fedoraproje 4.8 MB/s | 937 kB 00:00 Red Hat Enterprise Linux - BaseOS 50 MB/s | 66 MB 00:01 Red Hat Enterprise Linux - AppStream 46 MB/s | 59 MB 00:01 Red Hat Enterprise Linux - CodeReady Linux Buil 12 MB/s | 8.9 MB 00:00 Extra Packages for Enterprise Linux 8 - x86_64 14 MB/s | 16 MB 00:01 Dependencies resolved. =========================================================================================== Package Arch Version Repository Size =========================================================================================== Installing: bash x86_64 4.4.20-4.el8_6 rhel-baseos 1.5 M bzip2 x86_64 1.0.6-26.el8 rhel-baseos 60 k coreutils x86_64 8.30-15.el8 rhel-baseos 1.2 M cpio x86_64 2.13-8.el8 copr_base 288 k diffutils x86_64 3.6-6.el8 rhel-baseos 359 k epel-rpm-macros noarch 8-41 epel 27 k findutils x86_64 1:4.6.0-21.el8 rhel-baseos 527 k gawk x86_64 4.2.1-4.el8 rhel-baseos 1.1 M gcc x86_64 8.5.0-20.el8 rhel-appstream 23 M gcc-c++ x86_64 8.5.0-20.el8 rhel-appstream 12 M grep x86_64 3.1-6.el8 rhel-baseos 274 k gzip x86_64 1.9-13.el8_5 rhel-baseos 167 k info x86_64 6.5-7.el8 rhel-baseos 198 k make x86_64 1:4.2.1-11.el8 rhel-baseos 498 k patch x86_64 2.7.6-11.el8 rhel-baseos 138 k redhat-release x86_64 8.9-0.1.el8 rhel-baseos 45 k redhat-rpm-config noarch 131-1.el8 rhel-appstream 91 k rpm-build x86_64 4.14.3-28.el8_9 rhel-appstream 174 k sed x86_64 4.5-5.el8 rhel-baseos 298 k tar x86_64 2:1.30-9.el8 rhel-baseos 839 k unzip x86_64 6.0-46.el8 rhel-baseos 196 k util-linux x86_64 2.32.1-43.el8 rhel-baseos 2.5 M which x86_64 2.21-20.el8 rhel-baseos 50 k xz x86_64 5.2.4-4.el8_6 rhel-baseos 153 k Installing dependencies: annobin x86_64 11.13-2.el8 rhel-appstream 972 k ansible-srpm-macros noarch 1-12.el8 epel 21 k audit-libs x86_64 3.0.7-5.el8 rhel-baseos 123 k basesystem noarch 11-5.el8 rhel-baseos 11 k binutils x86_64 2.30-123.el8 rhel-baseos 5.8 M brotli x86_64 1.0.6-3.el8 rhel-baseos 323 k bzip2-libs x86_64 1.0.6-26.el8 rhel-baseos 48 k ca-certificates noarch 2023.2.60_v7.0.306-80.0.el8_8 rhel-baseos 935 k chkconfig x86_64 1.19.2-1.el8 rhel-baseos 199 k coreutils-common x86_64 8.30-15.el8 rhel-baseos 2.0 M cpp x86_64 8.5.0-20.el8 rhel-appstream 10 M cracklib x86_64 2.9.6-15.el8 rhel-baseos 93 k cracklib-dicts x86_64 2.9.6-15.el8 rhel-baseos 4.0 M crypto-policies noarch 20230731-1.git3177e06.el8 rhel-baseos 64 k curl x86_64 7.61.1-33.el8 rhel-baseos 353 k cyrus-sasl-lib x86_64 2.1.27-6.el8_5 rhel-baseos 123 k dwz x86_64 0.12-10.el8 rhel-appstream 109 k efi-srpm-macros noarch 3-3.el8 rhel-appstream 22 k elfutils x86_64 0.189-3.el8 rhel-baseos 553 k elfutils-default-yama-scope noarch 0.189-3.el8 rhel-baseos 52 k elfutils-libelf x86_64 0.189-3.el8 rhel-baseos 232 k elfutils-libs x86_64 0.189-3.el8 rhel-baseos 303 k expat x86_64 2.2.5-11.el8 rhel-baseos 113 k file x86_64 5.33-25.el8 rhel-baseos 77 k file-libs x86_64 5.33-25.el8 rhel-baseos 544 k filesystem x86_64 3.8-6.el8 rhel-baseos 1.1 M fpc-srpm-macros noarch 1.3-1.el8 epel 8.2 k gc x86_64 7.6.4-3.el8 rhel-appstream 109 k gcc-plugin-annobin x86_64 8.5.0-20.el8 rhel-appstream 36 k gdb-headless x86_64 8.2-20.el8 rhel-appstream 3.7 M gdbm x86_64 1:1.18-2.el8 rhel-baseos 130 k gdbm-libs x86_64 1:1.18-2.el8 rhel-baseos 60 k ghc-srpm-macros noarch 1.4.2-7.el8 rhel-appstream 9.4 k glib2 x86_64 2.56.4-161.el8 rhel-baseos 2.5 M glibc x86_64 2.28-236.el8_9.12 rhel-baseos 2.2 M glibc-all-langpacks x86_64 2.28-236.el8_9.12 rhel-baseos 26 M glibc-common x86_64 2.28-236.el8_9.12 rhel-baseos 1.0 M glibc-devel x86_64 2.28-236.el8_9.12 rhel-baseos 86 k glibc-gconv-extra x86_64 2.28-236.el8_9.12 rhel-baseos 1.6 M glibc-headers x86_64 2.28-236.el8_9.12 rhel-baseos 491 k gmp x86_64 1:6.1.2-10.el8 rhel-baseos 321 k gnupg2 x86_64 2.2.20-3.el8_6 rhel-baseos 2.4 M gnutls x86_64 3.6.16-8.el8_9.1 rhel-baseos 1.0 M go-srpm-macros noarch 2-17.el8 rhel-appstream 13 k guile x86_64 5:2.0.14-7.el8 rhel-appstream 3.5 M ima-evm-utils x86_64 1.3.2-12.el8 rhel-baseos 64 k isl x86_64 0.16.1-6.el8 rhel-appstream 841 k kernel-headers x86_64 4.18.0-513.18.1.el8_9 rhel-baseos 11 M keyutils-libs x86_64 1.5.10-9.el8 rhel-baseos 34 k krb5-libs x86_64 1.18.2-26.el8_9 rhel-baseos 842 k libacl x86_64 2.2.53-1.el8 rhel-baseos 35 k libarchive x86_64 3.3.3-5.el8 rhel-baseos 360 k libassuan x86_64 2.5.1-3.el8 rhel-baseos 83 k libatomic_ops x86_64 7.6.2-3.el8 rhel-appstream 38 k libattr x86_64 2.4.48-3.el8 rhel-baseos 27 k libbabeltrace x86_64 1.5.4-4.el8 rhel-baseos 200 k libblkid x86_64 2.32.1-43.el8 rhel-baseos 220 k libcap x86_64 2.48-6.el8_9 rhel-baseos 74 k libcap-ng x86_64 0.7.11-1.el8 rhel-baseos 33 k libcom_err x86_64 1.45.6-5.el8 rhel-baseos 49 k libcurl x86_64 7.61.1-33.el8 rhel-baseos 303 k libdb x86_64 5.3.28-42.el8_4 rhel-baseos 751 k libdb-utils x86_64 5.3.28-42.el8_4 rhel-baseos 150 k libfdisk x86_64 2.32.1-43.el8 rhel-baseos 254 k libffi x86_64 3.1-24.el8 rhel-baseos 38 k libgcc x86_64 8.5.0-20.el8 rhel-baseos 81 k libgcrypt x86_64 1.8.5-7.el8_6 rhel-baseos 463 k libgomp x86_64 8.5.0-20.el8 rhel-baseos 208 k libgpg-error x86_64 1.31-1.el8 rhel-baseos 242 k libidn2 x86_64 2.2.0-1.el8 rhel-baseos 94 k libipt x86_64 1.6.1-8.el8 rhel-appstream 50 k libksba x86_64 1.3.5-9.el8_7 rhel-baseos 134 k libmount x86_64 2.32.1-43.el8 rhel-baseos 237 k libmpc x86_64 1.1.0-9.1.el8 rhel-appstream 61 k libnghttp2 x86_64 1.33.0-5.el8_9 rhel-baseos 78 k libnsl2 x86_64 1.2.0-2.20180605git4a062cf.el8 rhel-baseos 58 k libpkgconf x86_64 1.4.2-1.el8 rhel-baseos 35 k libpsl x86_64 0.20.2-6.el8 rhel-baseos 61 k libpwquality x86_64 1.4.4-6.el8 rhel-baseos 107 k libselinux x86_64 2.9-8.el8 rhel-baseos 166 k libsemanage x86_64 2.9-9.el8_6 rhel-baseos 168 k libsepol x86_64 2.9-3.el8 rhel-baseos 340 k libsigsegv x86_64 2.11-5.el8 rhel-baseos 30 k libsmartcols x86_64 2.32.1-43.el8 rhel-baseos 179 k libssh x86_64 0.9.6-13.el8_9 rhel-baseos 220 k libssh-config noarch 0.9.6-13.el8_9 rhel-baseos 21 k libstdc++ x86_64 8.5.0-20.el8 rhel-baseos 455 k libstdc++-devel x86_64 8.5.0-20.el8 rhel-appstream 2.1 M libtasn1 x86_64 4.13-4.el8_7 rhel-baseos 76 k libtirpc x86_64 1.1.4-8.el8 rhel-baseos 113 k libtool-ltdl x86_64 2.4.6-25.el8 rhel-baseos 58 k libunistring x86_64 0.9.9-3.el8 rhel-baseos 422 k libusbx x86_64 1.0.23-4.el8 rhel-baseos 74 k libutempter x86_64 1.1.6-14.el8 rhel-baseos 32 k libuuid x86_64 2.32.1-43.el8 rhel-baseos 99 k libverto x86_64 0.3.2-2.el8 rhel-baseos 24 k libxcrypt x86_64 4.1.1-6.el8 rhel-baseos 73 k libxcrypt-devel x86_64 4.1.1-6.el8 rhel-baseos 25 k libxml2 x86_64 2.9.7-18.el8_9 rhel-baseos 697 k libzstd x86_64 1.4.4-1.el8 rhel-baseos 266 k lua-libs x86_64 5.3.4-12.el8 rhel-baseos 118 k lua-srpm-macros noarch 1-3.el8 epel 8.1 k lz4-libs x86_64 1.8.3-3.el8_4 rhel-baseos 66 k mpfr x86_64 3.1.6-1.el8 rhel-baseos 221 k ncurses x86_64 6.1-10.20180224.el8 rhel-baseos 387 k ncurses-base noarch 6.1-10.20180224.el8 rhel-baseos 81 k ncurses-libs x86_64 6.1-10.20180224.el8 rhel-baseos 334 k nettle x86_64 3.4.1-7.el8 rhel-baseos 301 k npth x86_64 1.5-4.el8 rhel-baseos 26 k ocaml-srpm-macros noarch 5-4.el8 rhel-appstream 9.5 k openblas-srpm-macros noarch 2-2.el8 rhel-appstream 8.0 k openldap x86_64 2.4.46-18.el8 rhel-baseos 352 k openssl-libs x86_64 1:1.1.1k-12.el8_9 rhel-baseos 1.5 M p11-kit x86_64 0.23.22-1.el8 rhel-baseos 324 k p11-kit-trust x86_64 0.23.22-1.el8 rhel-baseos 137 k pam x86_64 1.3.1-27.el8 rhel-baseos 746 k pcre x86_64 8.42-6.el8 rhel-baseos 211 k pcre2 x86_64 10.32-3.el8_6 rhel-baseos 247 k perl-srpm-macros noarch 1-25.el8 rhel-appstream 11 k pkgconf x86_64 1.4.2-1.el8 rhel-baseos 38 k pkgconf-m4 noarch 1.4.2-1.el8 rhel-baseos 17 k pkgconf-pkg-config x86_64 1.4.2-1.el8 rhel-baseos 15 k platform-python x86_64 3.6.8-56.el8_9.3 rhel-baseos 87 k platform-python-setuptools noarch 39.2.0-7.el8 rhel-baseos 632 k popt x86_64 1.18-1.el8 rhel-baseos 61 k publicsuffix-list-dafsa noarch 20180723-1.el8 rhel-baseos 56 k python-rpm-macros noarch 3-45.el8 rhel-appstream 16 k python-srpm-macros noarch 3-45.el8 rhel-appstream 16 k python3-libs x86_64 3.6.8-56.el8_9.3 rhel-baseos 7.8 M python3-pip-wheel noarch 9.0.3-23.el8 rhel-baseos 866 k python3-rpm-macros noarch 3-45.el8 rhel-appstream 15 k python3-setuptools-wheel noarch 39.2.0-7.el8 rhel-baseos 289 k qt5-srpm-macros noarch 5.15.3-1.el8 rhel-appstream 11 k readline x86_64 7.0-10.el8 rhel-baseos 199 k rpm x86_64 4.14.3-28.el8_9 rhel-baseos 544 k rpm-build-libs x86_64 4.14.3-28.el8_9 rhel-baseos 157 k rpm-libs x86_64 4.14.3-28.el8_9 rhel-baseos 348 k rust-srpm-macros noarch 5-2.el8 rhel-appstream 9.3 k setup noarch 2.12.2-9.el8 rhel-baseos 181 k shadow-utils x86_64 2:4.6-19.el8 rhel-baseos 1.2 M sqlite-libs x86_64 3.26.0-19.el8_9 rhel-baseos 581 k systemd-libs x86_64 239-78.el8 rhel-baseos 1.1 M tpm2-tss x86_64 2.3.2-5.el8 rhel-baseos 275 k tzdata noarch 2024a-1.el8 rhel-baseos 475 k xz-libs x86_64 5.2.4-4.el8_6 rhel-baseos 94 k zip x86_64 3.0-23.el8 rhel-baseos 270 k zlib x86_64 1.2.11-25.el8 rhel-baseos 103 k zstd x86_64 1.4.4-1.el8 rhel-appstream 393 k Transaction Summary =========================================================================================== Install 172 Packages Total download size: 163 M Installed size: 814 M Downloading Packages: (1/172): cpio-2.13-8.el8.x86_64.rpm 4.4 MB/s | 288 kB 00:00 (2/172): bzip2-libs-1.0.6-26.el8.x86_64.rpm 242 kB/s | 48 kB 00:00 (3/172): cracklib-2.9.6-15.el8.x86_64.rpm 408 kB/s | 93 kB 00:00 (4/172): bzip2-1.0.6-26.el8.x86_64.rpm 185 kB/s | 60 kB 00:00 (5/172): grep-3.1-6.el8.x86_64.rpm 1.8 MB/s | 274 kB 00:00 (6/172): libassuan-2.5.1-3.el8.x86_64.rpm 360 kB/s | 83 kB 00:00 (7/172): libattr-2.4.48-3.el8.x86_64.rpm 155 kB/s | 27 kB 00:00 (8/172): cracklib-dicts-2.9.6-15.el8.x86_64.rpm 7.8 MB/s | 4.0 MB 00:00 (9/172): libsigsegv-2.11-5.el8.x86_64.rpm 205 kB/s | 30 kB 00:00 (10/172): libunistring-0.9.9-3.el8.x86_64.rpm 3.9 MB/s | 422 kB 00:00 (11/172): npth-1.5-4.el8.x86_64.rpm 370 kB/s | 26 kB 00:00 (12/172): mpfr-3.1.6-1.el8.x86_64.rpm 1.7 MB/s | 221 kB 00:00 (13/172): libutempter-1.1.6-14.el8.x86_64.rpm 232 kB/s | 32 kB 00:00 (14/172): pkgconf-1.4.2-1.el8.x86_64.rpm 436 kB/s | 38 kB 00:00 (15/172): pkgconf-pkg-config-1.4.2-1.el8.x86_64 137 kB/s | 15 kB 00:00 (16/172): readline-7.0-10.el8.x86_64.rpm 1.5 MB/s | 199 kB 00:00 (17/172): zip-3.0-23.el8.x86_64.rpm 2.4 MB/s | 270 kB 00:00 (18/172): basesystem-11-5.el8.noarch.rpm 87 kB/s | 11 kB 00:00 (19/172): libgpg-error-1.31-1.el8.x86_64.rpm 2.4 MB/s | 242 kB 00:00 (20/172): libnsl2-1.2.0-2.20180605git4a062cf.el 473 kB/s | 58 kB 00:00 (21/172): libpkgconf-1.4.2-1.el8.x86_64.rpm 248 kB/s | 35 kB 00:00 (22/172): libacl-2.2.53-1.el8.x86_64.rpm 121 kB/s | 35 kB 00:00 (23/172): libtool-ltdl-2.4.6-25.el8.x86_64.rpm 639 kB/s | 58 kB 00:00 (24/172): gmp-6.1.2-10.el8.x86_64.rpm 3.7 MB/s | 321 kB 00:00 (25/172): pkgconf-m4-1.4.2-1.el8.noarch.rpm 121 kB/s | 17 kB 00:00 (26/172): publicsuffix-list-dafsa-20180723-1.el 464 kB/s | 56 kB 00:00 (27/172): diffutils-3.6-6.el8.x86_64.rpm 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coreutils-8.30-15.el8.x86_64.rpm 8.2 MB/s | 1.2 MB 00:00 (74/172): expat-2.2.5-11.el8.x86_64.rpm 838 kB/s | 113 kB 00:00 (75/172): glib2-2.56.4-161.el8.x86_64.rpm 20 MB/s | 2.5 MB 00:00 (76/172): coreutils-common-8.30-15.el8.x86_64.r 7.9 MB/s | 2.0 MB 00:00 (77/172): libarchive-3.3.3-5.el8.x86_64.rpm 4.8 MB/s | 360 kB 00:00 (78/172): libffi-3.1-24.el8.x86_64.rpm 497 kB/s | 38 kB 00:00 (79/172): libselinux-2.9-8.el8.x86_64.rpm 2.0 MB/s | 166 kB 00:00 (80/172): libpwquality-1.4.4-6.el8.x86_64.rpm 426 kB/s | 107 kB 00:00 (81/172): python3-setuptools-wheel-39.2.0-7.el8 1.3 MB/s | 289 kB 00:00 (82/172): platform-python-setuptools-39.2.0-7.e 2.2 MB/s | 632 kB 00:00 (83/172): setup-2.12.2-9.el8.noarch.rpm 1.3 MB/s | 181 kB 00:00 (84/172): audit-libs-3.0.7-5.el8.x86_64.rpm 1.6 MB/s | 123 kB 00:00 (85/172): tar-1.30-9.el8.x86_64.rpm 6.3 MB/s | 839 kB 00:00 (86/172): ca-certificates-2023.2.60_v7.0.306-80 12 MB/s | 935 kB 00:00 (87/172): chkconfig-1.19.2-1.el8.x86_64.rpm 1.6 MB/s | 199 kB 00:00 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platform-python-3.6.8-56.el8_9.3.x86 920 kB/s | 87 kB 00:00 (118/172): ncurses-6.1-10.20180224.el8.x86_64.r 1.8 MB/s | 387 kB 00:00 (119/172): redhat-release-8.9-0.1.el8.x86_64.rp 409 kB/s | 45 kB 00:00 (120/172): python3-pip-wheel-9.0.3-23.el8.noarc 4.8 MB/s | 866 kB 00:00 (121/172): sqlite-libs-3.26.0-19.el8_9.x86_64.r 7.5 MB/s | 581 kB 00:00 (122/172): shadow-utils-4.6-19.el8.x86_64.rpm 9.1 MB/s | 1.2 MB 00:00 (123/172): python3-libs-3.6.8-56.el8_9.3.x86_64 29 MB/s | 7.8 MB 00:00 (124/172): tpm2-tss-2.3.2-5.el8.x86_64.rpm 3.4 MB/s | 275 kB 00:00 (125/172): systemd-libs-239-78.el8.x86_64.rpm 10 MB/s | 1.1 MB 00:00 (126/172): zlib-1.2.11-25.el8.x86_64.rpm 1.1 MB/s | 103 kB 00:00 (127/172): libssh-config-0.9.6-13.el8_9.noarch. 293 kB/s | 21 kB 00:00 (128/172): gnutls-3.6.16-8.el8_9.1.x86_64.rpm 5.9 MB/s | 1.0 MB 00:00 (129/172): rpm-4.14.3-28.el8_9.x86_64.rpm 3.8 MB/s | 544 kB 00:00 (130/172): rpm-build-libs-4.14.3-28.el8_9.x86_6 2.1 MB/s | 157 kB 00:00 (131/172): 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(160/172): gcc-plugin-annobin-8.5.0-20.el8.x86_ 297 kB/s | 36 kB 00:00 (161/172): annobin-11.13-2.el8.x86_64.rpm 5.6 MB/s | 972 kB 00:00 (162/172): gcc-c++-8.5.0-20.el8.x86_64.rpm 30 MB/s | 12 MB 00:00 (163/172): python-rpm-macros-3-45.el8.noarch.rp 18 kB/s | 16 kB 00:00 (164/172): gcc-8.5.0-20.el8.x86_64.rpm 42 MB/s | 23 MB 00:00 (165/172): cpp-8.5.0-20.el8.x86_64.rpm 16 MB/s | 10 MB 00:00 (166/172): gdb-headless-8.2-20.el8.x86_64.rpm 10 MB/s | 3.7 MB 00:00 (167/172): libstdc++-devel-8.5.0-20.el8.x86_64. 12 MB/s | 2.1 MB 00:00 (168/172): rpm-build-4.14.3-28.el8_9.x86_64.rpm 777 kB/s | 174 kB 00:00 (169/172): ansible-srpm-macros-1-12.el8.noarch. 107 kB/s | 21 kB 00:00 (170/172): epel-rpm-macros-8-41.noarch.rpm 135 kB/s | 27 kB 00:00 (171/172): lua-srpm-macros-1-3.el8.noarch.rpm 118 kB/s | 8.1 kB 00:00 (172/172): fpc-srpm-macros-1.3-1.el8.noarch.rpm 53 kB/s | 8.2 kB 00:00 -------------------------------------------------------------------------------- Total 18 MB/s | 163 MB 00:09 Red Hat Enterprise Linux - BaseOS 3.1 MB/s | 3.1 kB 00:00 Traceback (most recent call last): File "/usr/bin/dnf-3", line 62, in main.user_main(sys.argv[1:], exit_code=True) File "/usr/lib/python3.12/site-packages/dnf/cli/main.py", line 201, in user_main errcode = main(args) ^^^^^^^^^^ File "/usr/lib/python3.12/site-packages/dnf/cli/main.py", line 67, in main return _main(base, args, cli_class, option_parser_class) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/site-packages/dnf/cli/main.py", line 106, in _main return cli_run(cli, base) ^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/site-packages/dnf/cli/main.py", line 130, in cli_run ret = resolving(cli, base) ^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/site-packages/dnf/cli/main.py", line 176, in resolving base.do_transaction(display=displays) File "/usr/lib/python3.12/site-packages/dnf/cli/cli.py", line 238, in do_transaction self.gpgsigcheck(install_pkgs) File "/usr/lib/python3.12/site-packages/dnf/cli/cli.py", line 294, in gpgsigcheck self._get_key_for_package(po, fn) File "/usr/lib/python3.12/site-packages/dnf/base.py", line 2531, in _get_key_for_package keys = dnf.crypto.retrieve(keyurl, repo) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/site-packages/dnf/crypto.py", line 137, in retrieve keyinfos = rawkey2infos(handle) ^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/site-packages/dnf/crypto.py", line 127, in rawkey2infos keys = libdnf.repo.Key.keysFromFd(key_fo.fileno()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.12/site-packages/libdnf/repo.py", line 341, in keysFromFd return _repo.Key_keysFromFd(fileDescriptor) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ RuntimeError: Parsing armored OpenPGP packet(s) failed WARNING: DNF command failed, retrying, attempt #2, sleeping 10s No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. 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Copr repository 29 kB/s | 2.2 kB 00:00 Additional repo https_copr_be_cloud_fedoraproje 65 kB/s | 2.2 kB 00:00 Red Hat Enterprise Linux - BaseOS 8.6 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux - AppStream 24 kB/s | 4.5 kB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 21 kB/s | 4.5 kB 00:00 Extra Packages for Enterprise Linux 8 - x86_64 691 kB/s | 28 kB 00:00 Dependencies resolved. =========================================================================================== Package Arch Version Repository Size =========================================================================================== Installing: bash x86_64 4.4.20-4.el8_6 rhel-baseos 1.5 M bzip2 x86_64 1.0.6-26.el8 rhel-baseos 60 k coreutils x86_64 8.30-15.el8 rhel-baseos 1.2 M cpio x86_64 2.13-8.el8 copr_base 288 k diffutils x86_64 3.6-6.el8 rhel-baseos 359 k epel-rpm-macros noarch 8-41 epel 27 k findutils x86_64 1:4.6.0-21.el8 rhel-baseos 527 k gawk x86_64 4.2.1-4.el8 rhel-baseos 1.1 M gcc x86_64 8.5.0-20.el8 rhel-appstream 23 M gcc-c++ x86_64 8.5.0-20.el8 rhel-appstream 12 M grep x86_64 3.1-6.el8 rhel-baseos 274 k gzip x86_64 1.9-13.el8_5 rhel-baseos 167 k info x86_64 6.5-7.el8 rhel-baseos 198 k make x86_64 1:4.2.1-11.el8 rhel-baseos 498 k patch x86_64 2.7.6-11.el8 rhel-baseos 138 k redhat-release x86_64 8.9-0.1.el8 rhel-baseos 45 k redhat-rpm-config noarch 131-1.el8 rhel-appstream 91 k rpm-build x86_64 4.14.3-28.el8_9 rhel-appstream 174 k sed x86_64 4.5-5.el8 rhel-baseos 298 k tar x86_64 2:1.30-9.el8 rhel-baseos 839 k unzip x86_64 6.0-46.el8 rhel-baseos 196 k util-linux x86_64 2.32.1-43.el8 rhel-baseos 2.5 M which x86_64 2.21-20.el8 rhel-baseos 50 k xz x86_64 5.2.4-4.el8_6 rhel-baseos 153 k Installing dependencies: annobin x86_64 11.13-2.el8 rhel-appstream 972 k ansible-srpm-macros noarch 1-12.el8 epel 21 k audit-libs x86_64 3.0.7-5.el8 rhel-baseos 123 k basesystem noarch 11-5.el8 rhel-baseos 11 k binutils x86_64 2.30-123.el8 rhel-baseos 5.8 M brotli x86_64 1.0.6-3.el8 rhel-baseos 323 k bzip2-libs x86_64 1.0.6-26.el8 rhel-baseos 48 k ca-certificates noarch 2023.2.60_v7.0.306-80.0.el8_8 rhel-baseos 935 k chkconfig x86_64 1.19.2-1.el8 rhel-baseos 199 k coreutils-common x86_64 8.30-15.el8 rhel-baseos 2.0 M cpp x86_64 8.5.0-20.el8 rhel-appstream 10 M cracklib x86_64 2.9.6-15.el8 rhel-baseos 93 k cracklib-dicts x86_64 2.9.6-15.el8 rhel-baseos 4.0 M crypto-policies noarch 20230731-1.git3177e06.el8 rhel-baseos 64 k curl x86_64 7.61.1-33.el8 rhel-baseos 353 k cyrus-sasl-lib x86_64 2.1.27-6.el8_5 rhel-baseos 123 k dwz x86_64 0.12-10.el8 rhel-appstream 109 k efi-srpm-macros noarch 3-3.el8 rhel-appstream 22 k elfutils x86_64 0.189-3.el8 rhel-baseos 553 k elfutils-default-yama-scope noarch 0.189-3.el8 rhel-baseos 52 k elfutils-libelf x86_64 0.189-3.el8 rhel-baseos 232 k elfutils-libs x86_64 0.189-3.el8 rhel-baseos 303 k expat x86_64 2.2.5-11.el8 rhel-baseos 113 k file x86_64 5.33-25.el8 rhel-baseos 77 k file-libs x86_64 5.33-25.el8 rhel-baseos 544 k filesystem x86_64 3.8-6.el8 rhel-baseos 1.1 M fpc-srpm-macros noarch 1.3-1.el8 epel 8.2 k gc x86_64 7.6.4-3.el8 rhel-appstream 109 k gcc-plugin-annobin x86_64 8.5.0-20.el8 rhel-appstream 36 k gdb-headless x86_64 8.2-20.el8 rhel-appstream 3.7 M gdbm x86_64 1:1.18-2.el8 rhel-baseos 130 k gdbm-libs x86_64 1:1.18-2.el8 rhel-baseos 60 k ghc-srpm-macros noarch 1.4.2-7.el8 rhel-appstream 9.4 k glib2 x86_64 2.56.4-161.el8 rhel-baseos 2.5 M glibc x86_64 2.28-236.el8_9.12 rhel-baseos 2.2 M glibc-all-langpacks x86_64 2.28-236.el8_9.12 rhel-baseos 26 M glibc-common x86_64 2.28-236.el8_9.12 rhel-baseos 1.0 M glibc-devel x86_64 2.28-236.el8_9.12 rhel-baseos 86 k glibc-gconv-extra x86_64 2.28-236.el8_9.12 rhel-baseos 1.6 M glibc-headers x86_64 2.28-236.el8_9.12 rhel-baseos 491 k gmp x86_64 1:6.1.2-10.el8 rhel-baseos 321 k gnupg2 x86_64 2.2.20-3.el8_6 rhel-baseos 2.4 M gnutls x86_64 3.6.16-8.el8_9.1 rhel-baseos 1.0 M go-srpm-macros noarch 2-17.el8 rhel-appstream 13 k guile x86_64 5:2.0.14-7.el8 rhel-appstream 3.5 M ima-evm-utils x86_64 1.3.2-12.el8 rhel-baseos 64 k isl x86_64 0.16.1-6.el8 rhel-appstream 841 k kernel-headers x86_64 4.18.0-513.18.1.el8_9 rhel-baseos 11 M keyutils-libs x86_64 1.5.10-9.el8 rhel-baseos 34 k krb5-libs x86_64 1.18.2-26.el8_9 rhel-baseos 842 k libacl x86_64 2.2.53-1.el8 rhel-baseos 35 k libarchive x86_64 3.3.3-5.el8 rhel-baseos 360 k libassuan x86_64 2.5.1-3.el8 rhel-baseos 83 k libatomic_ops x86_64 7.6.2-3.el8 rhel-appstream 38 k libattr x86_64 2.4.48-3.el8 rhel-baseos 27 k libbabeltrace x86_64 1.5.4-4.el8 rhel-baseos 200 k libblkid x86_64 2.32.1-43.el8 rhel-baseos 220 k libcap x86_64 2.48-6.el8_9 rhel-baseos 74 k libcap-ng x86_64 0.7.11-1.el8 rhel-baseos 33 k libcom_err x86_64 1.45.6-5.el8 rhel-baseos 49 k libcurl x86_64 7.61.1-33.el8 rhel-baseos 303 k libdb x86_64 5.3.28-42.el8_4 rhel-baseos 751 k libdb-utils x86_64 5.3.28-42.el8_4 rhel-baseos 150 k libfdisk x86_64 2.32.1-43.el8 rhel-baseos 254 k libffi x86_64 3.1-24.el8 rhel-baseos 38 k libgcc x86_64 8.5.0-20.el8 rhel-baseos 81 k libgcrypt x86_64 1.8.5-7.el8_6 rhel-baseos 463 k libgomp x86_64 8.5.0-20.el8 rhel-baseos 208 k libgpg-error x86_64 1.31-1.el8 rhel-baseos 242 k libidn2 x86_64 2.2.0-1.el8 rhel-baseos 94 k libipt x86_64 1.6.1-8.el8 rhel-appstream 50 k libksba x86_64 1.3.5-9.el8_7 rhel-baseos 134 k libmount x86_64 2.32.1-43.el8 rhel-baseos 237 k libmpc x86_64 1.1.0-9.1.el8 rhel-appstream 61 k libnghttp2 x86_64 1.33.0-5.el8_9 rhel-baseos 78 k libnsl2 x86_64 1.2.0-2.20180605git4a062cf.el8 rhel-baseos 58 k libpkgconf x86_64 1.4.2-1.el8 rhel-baseos 35 k libpsl x86_64 0.20.2-6.el8 rhel-baseos 61 k libpwquality x86_64 1.4.4-6.el8 rhel-baseos 107 k libselinux x86_64 2.9-8.el8 rhel-baseos 166 k libsemanage x86_64 2.9-9.el8_6 rhel-baseos 168 k libsepol x86_64 2.9-3.el8 rhel-baseos 340 k libsigsegv x86_64 2.11-5.el8 rhel-baseos 30 k libsmartcols x86_64 2.32.1-43.el8 rhel-baseos 179 k libssh x86_64 0.9.6-13.el8_9 rhel-baseos 220 k libssh-config noarch 0.9.6-13.el8_9 rhel-baseos 21 k libstdc++ x86_64 8.5.0-20.el8 rhel-baseos 455 k libstdc++-devel x86_64 8.5.0-20.el8 rhel-appstream 2.1 M libtasn1 x86_64 4.13-4.el8_7 rhel-baseos 76 k libtirpc x86_64 1.1.4-8.el8 rhel-baseos 113 k libtool-ltdl x86_64 2.4.6-25.el8 rhel-baseos 58 k libunistring x86_64 0.9.9-3.el8 rhel-baseos 422 k libusbx x86_64 1.0.23-4.el8 rhel-baseos 74 k libutempter x86_64 1.1.6-14.el8 rhel-baseos 32 k libuuid x86_64 2.32.1-43.el8 rhel-baseos 99 k libverto x86_64 0.3.2-2.el8 rhel-baseos 24 k libxcrypt x86_64 4.1.1-6.el8 rhel-baseos 73 k libxcrypt-devel x86_64 4.1.1-6.el8 rhel-baseos 25 k libxml2 x86_64 2.9.7-18.el8_9 rhel-baseos 697 k libzstd x86_64 1.4.4-1.el8 rhel-baseos 266 k lua-libs x86_64 5.3.4-12.el8 rhel-baseos 118 k lua-srpm-macros noarch 1-3.el8 epel 8.1 k lz4-libs x86_64 1.8.3-3.el8_4 rhel-baseos 66 k mpfr x86_64 3.1.6-1.el8 rhel-baseos 221 k ncurses x86_64 6.1-10.20180224.el8 rhel-baseos 387 k ncurses-base noarch 6.1-10.20180224.el8 rhel-baseos 81 k ncurses-libs x86_64 6.1-10.20180224.el8 rhel-baseos 334 k nettle x86_64 3.4.1-7.el8 rhel-baseos 301 k npth x86_64 1.5-4.el8 rhel-baseos 26 k ocaml-srpm-macros noarch 5-4.el8 rhel-appstream 9.5 k openblas-srpm-macros noarch 2-2.el8 rhel-appstream 8.0 k openldap x86_64 2.4.46-18.el8 rhel-baseos 352 k openssl-libs x86_64 1:1.1.1k-12.el8_9 rhel-baseos 1.5 M p11-kit x86_64 0.23.22-1.el8 rhel-baseos 324 k p11-kit-trust x86_64 0.23.22-1.el8 rhel-baseos 137 k pam x86_64 1.3.1-27.el8 rhel-baseos 746 k pcre x86_64 8.42-6.el8 rhel-baseos 211 k pcre2 x86_64 10.32-3.el8_6 rhel-baseos 247 k perl-srpm-macros noarch 1-25.el8 rhel-appstream 11 k pkgconf x86_64 1.4.2-1.el8 rhel-baseos 38 k pkgconf-m4 noarch 1.4.2-1.el8 rhel-baseos 17 k pkgconf-pkg-config x86_64 1.4.2-1.el8 rhel-baseos 15 k platform-python x86_64 3.6.8-56.el8_9.3 rhel-baseos 87 k platform-python-setuptools noarch 39.2.0-7.el8 rhel-baseos 632 k popt x86_64 1.18-1.el8 rhel-baseos 61 k publicsuffix-list-dafsa noarch 20180723-1.el8 rhel-baseos 56 k python-rpm-macros noarch 3-45.el8 rhel-appstream 16 k python-srpm-macros noarch 3-45.el8 rhel-appstream 16 k python3-libs x86_64 3.6.8-56.el8_9.3 rhel-baseos 7.8 M python3-pip-wheel noarch 9.0.3-23.el8 rhel-baseos 866 k python3-rpm-macros noarch 3-45.el8 rhel-appstream 15 k python3-setuptools-wheel noarch 39.2.0-7.el8 rhel-baseos 289 k qt5-srpm-macros noarch 5.15.3-1.el8 rhel-appstream 11 k readline x86_64 7.0-10.el8 rhel-baseos 199 k rpm x86_64 4.14.3-28.el8_9 rhel-baseos 544 k rpm-build-libs x86_64 4.14.3-28.el8_9 rhel-baseos 157 k rpm-libs x86_64 4.14.3-28.el8_9 rhel-baseos 348 k rust-srpm-macros noarch 5-2.el8 rhel-appstream 9.3 k setup noarch 2.12.2-9.el8 rhel-baseos 181 k shadow-utils x86_64 2:4.6-19.el8 rhel-baseos 1.2 M sqlite-libs x86_64 3.26.0-19.el8_9 rhel-baseos 581 k systemd-libs x86_64 239-78.el8 rhel-baseos 1.1 M tpm2-tss x86_64 2.3.2-5.el8 rhel-baseos 275 k tzdata noarch 2024a-1.el8 rhel-baseos 475 k xz-libs x86_64 5.2.4-4.el8_6 rhel-baseos 94 k zip x86_64 3.0-23.el8 rhel-baseos 270 k zlib x86_64 1.2.11-25.el8 rhel-baseos 103 k zstd x86_64 1.4.4-1.el8 rhel-appstream 393 k Transaction Summary =========================================================================================== Install 172 Packages Total size: 163 M Installed size: 814 M Downloading Packages: [SKIPPED] cpio-2.13-8.el8.x86_64.rpm: Already downloaded [SKIPPED] bzip2-1.0.6-26.el8.x86_64.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.6-26.el8.x86_64.rpm: Already downloaded [SKIPPED] cracklib-2.9.6-15.el8.x86_64.rpm: Already downloaded [SKIPPED] cracklib-dicts-2.9.6-15.el8.x86_64.rpm: Already downloaded [SKIPPED] grep-3.1-6.el8.x86_64.rpm: Already downloaded [SKIPPED] libassuan-2.5.1-3.el8.x86_64.rpm: Already downloaded [SKIPPED] libattr-2.4.48-3.el8.x86_64.rpm: Already downloaded [SKIPPED] libsigsegv-2.11-5.el8.x86_64.rpm: Already downloaded [SKIPPED] libunistring-0.9.9-3.el8.x86_64.rpm: Already downloaded [SKIPPED] libutempter-1.1.6-14.el8.x86_64.rpm: Already downloaded [SKIPPED] mpfr-3.1.6-1.el8.x86_64.rpm: Already downloaded [SKIPPED] npth-1.5-4.el8.x86_64.rpm: Already downloaded [SKIPPED] pkgconf-1.4.2-1.el8.x86_64.rpm: Already downloaded [SKIPPED] pkgconf-pkg-config-1.4.2-1.el8.x86_64.rpm: Already downloaded [SKIPPED] readline-7.0-10.el8.x86_64.rpm: Already downloaded [SKIPPED] zip-3.0-23.el8.x86_64.rpm: Already downloaded [SKIPPED] basesystem-11-5.el8.noarch.rpm: Already downloaded [SKIPPED] libacl-2.2.53-1.el8.x86_64.rpm: Already downloaded [SKIPPED] libgpg-error-1.31-1.el8.x86_64.rpm: Already downloaded [SKIPPED] libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64.rpm: Already downloaded [SKIPPED] libpkgconf-1.4.2-1.el8.x86_64.rpm: Already downloaded [SKIPPED] libtool-ltdl-2.4.6-25.el8.x86_64.rpm: Already downloaded [SKIPPED] pkgconf-m4-1.4.2-1.el8.noarch.rpm: Already downloaded [SKIPPED] publicsuffix-list-dafsa-20180723-1.el8.noarch.rpm: Already downloaded [SKIPPED] gmp-6.1.2-10.el8.x86_64.rpm: Already downloaded [SKIPPED] diffutils-3.6-6.el8.x86_64.rpm: Already downloaded [SKIPPED] libidn2-2.2.0-1.el8.x86_64.rpm: Already downloaded [SKIPPED] patch-2.7.6-11.el8.x86_64.rpm: Already downloaded [SKIPPED] libusbx-1.0.23-4.el8.x86_64.rpm: Already downloaded [SKIPPED] libzstd-1.4.4-1.el8.x86_64.rpm: Already downloaded [SKIPPED] libpsl-0.20.2-6.el8.x86_64.rpm: Already downloaded [SKIPPED] p11-kit-trust-0.23.22-1.el8.x86_64.rpm: Already downloaded [SKIPPED] popt-1.18-1.el8.x86_64.rpm: Already downloaded [SKIPPED] brotli-1.0.6-3.el8.x86_64.rpm: Already downloaded [SKIPPED] ima-evm-utils-1.3.2-12.el8.x86_64.rpm: Already downloaded [SKIPPED] lz4-libs-1.8.3-3.el8_4.x86_64.rpm: Already downloaded [SKIPPED] p11-kit-0.23.22-1.el8.x86_64.rpm: Already downloaded [SKIPPED] filesystem-3.8-6.el8.x86_64.rpm: Already downloaded [SKIPPED] libcap-ng-0.7.11-1.el8.x86_64.rpm: Already downloaded [SKIPPED] libdb-5.3.28-42.el8_4.x86_64.rpm: Already downloaded [SKIPPED] libdb-utils-5.3.28-42.el8_4.x86_64.rpm: Already downloaded [SKIPPED] libxcrypt-4.1.1-6.el8.x86_64.rpm: Already downloaded [SKIPPED] libxcrypt-devel-4.1.1-6.el8.x86_64.rpm: Already downloaded [SKIPPED] nettle-3.4.1-7.el8.x86_64.rpm: Already downloaded [SKIPPED] openldap-2.4.46-18.el8.x86_64.rpm: Already downloaded [SKIPPED] pcre-8.42-6.el8.x86_64.rpm: Already downloaded [SKIPPED] cyrus-sasl-lib-2.1.27-6.el8_5.x86_64.rpm: Already downloaded [SKIPPED] gzip-1.9-13.el8_5.x86_64.rpm: Already downloaded [SKIPPED] keyutils-libs-1.5.10-9.el8.x86_64.rpm: Already downloaded [SKIPPED] libsepol-2.9-3.el8.x86_64.rpm: Already downloaded [SKIPPED] lua-libs-5.3.4-12.el8.x86_64.rpm: Already downloaded [SKIPPED] gawk-4.2.1-4.el8.x86_64.rpm: Already downloaded [SKIPPED] info-6.5-7.el8.x86_64.rpm: Already downloaded [SKIPPED] make-4.2.1-11.el8.x86_64.rpm: Already downloaded [SKIPPED] sed-4.5-5.el8.x86_64.rpm: Already downloaded [SKIPPED] unzip-6.0-46.el8.x86_64.rpm: Already downloaded [SKIPPED] xz-5.2.4-4.el8_6.x86_64.rpm: Already downloaded [SKIPPED] xz-libs-5.2.4-4.el8_6.x86_64.rpm: Already downloaded [SKIPPED] bash-4.4.20-4.el8_6.x86_64.rpm: Already downloaded [SKIPPED] gdbm-libs-1.18-2.el8.x86_64.rpm: Already downloaded [SKIPPED] gnupg2-2.2.20-3.el8_6.x86_64.rpm: Already downloaded [SKIPPED] libbabeltrace-1.5.4-4.el8.x86_64.rpm: Already downloaded [SKIPPED] libcom_err-1.45.6-5.el8.x86_64.rpm: Already downloaded [SKIPPED] libgcrypt-1.8.5-7.el8_6.x86_64.rpm: Already downloaded [SKIPPED] libsemanage-2.9-9.el8_6.x86_64.rpm: Already downloaded [SKIPPED] libtirpc-1.1.4-8.el8.x86_64.rpm: Already downloaded [SKIPPED] libverto-0.3.2-2.el8.x86_64.rpm: Already downloaded [SKIPPED] pcre2-10.32-3.el8_6.x86_64.rpm: Already downloaded [SKIPPED] gdbm-1.18-2.el8.x86_64.rpm: Already downloaded [SKIPPED] libksba-1.3.5-9.el8_7.x86_64.rpm: Already downloaded [SKIPPED] libtasn1-4.13-4.el8_7.x86_64.rpm: Already downloaded [SKIPPED] coreutils-8.30-15.el8.x86_64.rpm: Already downloaded [SKIPPED] coreutils-common-8.30-15.el8.x86_64.rpm: Already downloaded [SKIPPED] expat-2.2.5-11.el8.x86_64.rpm: Already downloaded [SKIPPED] glib2-2.56.4-161.el8.x86_64.rpm: Already downloaded [SKIPPED] libarchive-3.3.3-5.el8.x86_64.rpm: Already downloaded [SKIPPED] libffi-3.1-24.el8.x86_64.rpm: Already downloaded [SKIPPED] libpwquality-1.4.4-6.el8.x86_64.rpm: Already downloaded [SKIPPED] libselinux-2.9-8.el8.x86_64.rpm: Already downloaded [SKIPPED] platform-python-setuptools-39.2.0-7.el8.noarch.rpm: Already downloaded [SKIPPED] python3-setuptools-wheel-39.2.0-7.el8.noarch.rpm: Already downloaded [SKIPPED] setup-2.12.2-9.el8.noarch.rpm: Already downloaded [SKIPPED] tar-1.30-9.el8.x86_64.rpm: Already downloaded [SKIPPED] audit-libs-3.0.7-5.el8.x86_64.rpm: Already downloaded [SKIPPED] binutils-2.30-123.el8.x86_64.rpm: Already downloaded [SKIPPED] ca-certificates-2023.2.60_v7.0.306-80.0.el8_8.noarch.rpm: Already downloaded [SKIPPED] chkconfig-1.19.2-1.el8.x86_64.rpm: Already downloaded [SKIPPED] crypto-policies-20230731-1.git3177e06.el8.noarch.rpm: Already downloaded [SKIPPED] curl-7.61.1-33.el8.x86_64.rpm: Already 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pam-1.3.1-27.el8.x86_64.rpm: Already downloaded [SKIPPED] util-linux-2.32.1-43.el8.x86_64.rpm: Already downloaded [SKIPPED] which-2.21-20.el8.x86_64.rpm: Already downloaded [SKIPPED] elfutils-default-yama-scope-0.189-3.el8.noarch.rpm: Already downloaded [SKIPPED] krb5-libs-1.18.2-26.el8_9.x86_64.rpm: Already downloaded [SKIPPED] libblkid-2.32.1-43.el8.x86_64.rpm: Already downloaded [SKIPPED] libcap-2.48-6.el8_9.x86_64.rpm: Already downloaded [SKIPPED] libfdisk-2.32.1-43.el8.x86_64.rpm: Already downloaded [SKIPPED] libxml2-2.9.7-18.el8_9.x86_64.rpm: Already downloaded [SKIPPED] ncurses-6.1-10.20180224.el8.x86_64.rpm: Already downloaded [SKIPPED] ncurses-base-6.1-10.20180224.el8.noarch.rpm: Already downloaded [SKIPPED] openssl-libs-1.1.1k-12.el8_9.x86_64.rpm: Already downloaded [SKIPPED] platform-python-3.6.8-56.el8_9.3.x86_64.rpm: Already downloaded [SKIPPED] python3-libs-3.6.8-56.el8_9.3.x86_64.rpm: Already downloaded [SKIPPED] python3-pip-wheel-9.0.3-23.el8.noarch.rpm: Already 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gdb-headless-8.2-20.el8.x86_64.rpm: Already downloaded [SKIPPED] libstdc++-devel-8.5.0-20.el8.x86_64.rpm: Already downloaded [SKIPPED] rpm-build-4.14.3-28.el8_9.x86_64.rpm: Already downloaded [SKIPPED] ansible-srpm-macros-1-12.el8.noarch.rpm: Already downloaded [SKIPPED] epel-rpm-macros-8-41.noarch.rpm: Already downloaded [SKIPPED] fpc-srpm-macros-1.3-1.el8.noarch.rpm: Already downloaded [SKIPPED] lua-srpm-macros-1-3.el8.noarch.rpm: Already downloaded Red Hat Enterprise Linux - BaseOS 3.1 MB/s | 3.1 kB 00:00 Traceback (most recent call last): File "/usr/bin/dnf-3", line 62, in main.user_main(sys.argv[1:], exit_code=True) File "/usr/lib/python3.12/site-packages/dnf/cli/main.py", line 201, in user_main errcode = main(args) ^^^^^^^^^^ File "/usr/lib/python3.12/site-packages/dnf/cli/main.py", line 67, in main return _main(base, args, cli_class, option_parser_class) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/site-packages/dnf/cli/main.py", line 106, in _main return cli_run(cli, base) ^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/site-packages/dnf/cli/main.py", line 130, in cli_run ret = resolving(cli, base) ^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/site-packages/dnf/cli/main.py", line 176, in resolving base.do_transaction(display=displays) File "/usr/lib/python3.12/site-packages/dnf/cli/cli.py", line 238, in do_transaction self.gpgsigcheck(install_pkgs) File "/usr/lib/python3.12/site-packages/dnf/cli/cli.py", line 294, in gpgsigcheck self._get_key_for_package(po, fn) File "/usr/lib/python3.12/site-packages/dnf/base.py", line 2531, in _get_key_for_package keys = dnf.crypto.retrieve(keyurl, repo) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/site-packages/dnf/crypto.py", line 137, in retrieve keyinfos = rawkey2infos(handle) ^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/site-packages/dnf/crypto.py", line 127, in rawkey2infos keys = libdnf.repo.Key.keysFromFd(key_fo.fileno()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib64/python3.12/site-packages/libdnf/repo.py", line 341, in keysFromFd return _repo.Key_keysFromFd(fileDescriptor) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ RuntimeError: Parsing armored OpenPGP packet(s) failed WARNING: DNF command failed, retrying, attempt #3, sleeping 10s No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 46 kB/s | 2.2 kB 00:00 Additional repo https_copr_be_cloud_fedoraproje 48 kB/s | 2.2 kB 00:00 Red Hat Enterprise Linux - BaseOS 14 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux - AppStream 17 kB/s | 4.5 kB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 19 kB/s | 4.5 kB 00:00 Extra Packages for Enterprise Linux 8 - x86_64 839 kB/s | 28 kB 00:00 Dependencies resolved. =========================================================================================== Package Arch Version Repository Size =========================================================================================== Installing: bash x86_64 4.4.20-4.el8_6 rhel-baseos 1.5 M bzip2 x86_64 1.0.6-26.el8 rhel-baseos 60 k coreutils x86_64 8.30-15.el8 rhel-baseos 1.2 M cpio x86_64 2.13-8.el8 copr_base 288 k diffutils x86_64 3.6-6.el8 rhel-baseos 359 k epel-rpm-macros noarch 8-41 epel 27 k findutils x86_64 1:4.6.0-21.el8 rhel-baseos 527 k gawk x86_64 4.2.1-4.el8 rhel-baseos 1.1 M gcc x86_64 8.5.0-20.el8 rhel-appstream 23 M gcc-c++ x86_64 8.5.0-20.el8 rhel-appstream 12 M grep x86_64 3.1-6.el8 rhel-baseos 274 k gzip x86_64 1.9-13.el8_5 rhel-baseos 167 k info x86_64 6.5-7.el8 rhel-baseos 198 k make x86_64 1:4.2.1-11.el8 rhel-baseos 498 k patch x86_64 2.7.6-11.el8 rhel-baseos 138 k redhat-release x86_64 8.9-0.1.el8 rhel-baseos 45 k redhat-rpm-config noarch 131-1.el8 rhel-appstream 91 k rpm-build x86_64 4.14.3-28.el8_9 rhel-appstream 174 k sed x86_64 4.5-5.el8 rhel-baseos 298 k tar x86_64 2:1.30-9.el8 rhel-baseos 839 k unzip x86_64 6.0-46.el8 rhel-baseos 196 k util-linux x86_64 2.32.1-43.el8 rhel-baseos 2.5 M which x86_64 2.21-20.el8 rhel-baseos 50 k xz x86_64 5.2.4-4.el8_6 rhel-baseos 153 k Installing dependencies: annobin x86_64 11.13-2.el8 rhel-appstream 972 k ansible-srpm-macros noarch 1-12.el8 epel 21 k audit-libs x86_64 3.0.7-5.el8 rhel-baseos 123 k basesystem noarch 11-5.el8 rhel-baseos 11 k binutils x86_64 2.30-123.el8 rhel-baseos 5.8 M brotli x86_64 1.0.6-3.el8 rhel-baseos 323 k bzip2-libs x86_64 1.0.6-26.el8 rhel-baseos 48 k ca-certificates noarch 2023.2.60_v7.0.306-80.0.el8_8 rhel-baseos 935 k chkconfig x86_64 1.19.2-1.el8 rhel-baseos 199 k coreutils-common x86_64 8.30-15.el8 rhel-baseos 2.0 M cpp x86_64 8.5.0-20.el8 rhel-appstream 10 M cracklib x86_64 2.9.6-15.el8 rhel-baseos 93 k cracklib-dicts x86_64 2.9.6-15.el8 rhel-baseos 4.0 M crypto-policies noarch 20230731-1.git3177e06.el8 rhel-baseos 64 k curl x86_64 7.61.1-33.el8 rhel-baseos 353 k cyrus-sasl-lib x86_64 2.1.27-6.el8_5 rhel-baseos 123 k dwz x86_64 0.12-10.el8 rhel-appstream 109 k efi-srpm-macros noarch 3-3.el8 rhel-appstream 22 k elfutils x86_64 0.189-3.el8 rhel-baseos 553 k elfutils-default-yama-scope noarch 0.189-3.el8 rhel-baseos 52 k elfutils-libelf x86_64 0.189-3.el8 rhel-baseos 232 k elfutils-libs x86_64 0.189-3.el8 rhel-baseos 303 k expat x86_64 2.2.5-11.el8 rhel-baseos 113 k file x86_64 5.33-25.el8 rhel-baseos 77 k file-libs x86_64 5.33-25.el8 rhel-baseos 544 k filesystem x86_64 3.8-6.el8 rhel-baseos 1.1 M fpc-srpm-macros noarch 1.3-1.el8 epel 8.2 k gc x86_64 7.6.4-3.el8 rhel-appstream 109 k gcc-plugin-annobin x86_64 8.5.0-20.el8 rhel-appstream 36 k gdb-headless x86_64 8.2-20.el8 rhel-appstream 3.7 M gdbm x86_64 1:1.18-2.el8 rhel-baseos 130 k gdbm-libs x86_64 1:1.18-2.el8 rhel-baseos 60 k ghc-srpm-macros noarch 1.4.2-7.el8 rhel-appstream 9.4 k glib2 x86_64 2.56.4-161.el8 rhel-baseos 2.5 M glibc x86_64 2.28-236.el8_9.12 rhel-baseos 2.2 M glibc-all-langpacks x86_64 2.28-236.el8_9.12 rhel-baseos 26 M glibc-common x86_64 2.28-236.el8_9.12 rhel-baseos 1.0 M glibc-devel x86_64 2.28-236.el8_9.12 rhel-baseos 86 k glibc-gconv-extra x86_64 2.28-236.el8_9.12 rhel-baseos 1.6 M glibc-headers x86_64 2.28-236.el8_9.12 rhel-baseos 491 k gmp x86_64 1:6.1.2-10.el8 rhel-baseos 321 k gnupg2 x86_64 2.2.20-3.el8_6 rhel-baseos 2.4 M gnutls x86_64 3.6.16-8.el8_9.1 rhel-baseos 1.0 M go-srpm-macros noarch 2-17.el8 rhel-appstream 13 k guile x86_64 5:2.0.14-7.el8 rhel-appstream 3.5 M ima-evm-utils x86_64 1.3.2-12.el8 rhel-baseos 64 k isl x86_64 0.16.1-6.el8 rhel-appstream 841 k kernel-headers x86_64 4.18.0-513.18.1.el8_9 rhel-baseos 11 M keyutils-libs x86_64 1.5.10-9.el8 rhel-baseos 34 k krb5-libs x86_64 1.18.2-26.el8_9 rhel-baseos 842 k libacl x86_64 2.2.53-1.el8 rhel-baseos 35 k libarchive x86_64 3.3.3-5.el8 rhel-baseos 360 k libassuan x86_64 2.5.1-3.el8 rhel-baseos 83 k libatomic_ops x86_64 7.6.2-3.el8 rhel-appstream 38 k libattr x86_64 2.4.48-3.el8 rhel-baseos 27 k libbabeltrace x86_64 1.5.4-4.el8 rhel-baseos 200 k libblkid x86_64 2.32.1-43.el8 rhel-baseos 220 k libcap x86_64 2.48-6.el8_9 rhel-baseos 74 k libcap-ng x86_64 0.7.11-1.el8 rhel-baseos 33 k libcom_err x86_64 1.45.6-5.el8 rhel-baseos 49 k libcurl x86_64 7.61.1-33.el8 rhel-baseos 303 k libdb x86_64 5.3.28-42.el8_4 rhel-baseos 751 k libdb-utils x86_64 5.3.28-42.el8_4 rhel-baseos 150 k libfdisk x86_64 2.32.1-43.el8 rhel-baseos 254 k libffi x86_64 3.1-24.el8 rhel-baseos 38 k libgcc x86_64 8.5.0-20.el8 rhel-baseos 81 k libgcrypt x86_64 1.8.5-7.el8_6 rhel-baseos 463 k libgomp x86_64 8.5.0-20.el8 rhel-baseos 208 k libgpg-error x86_64 1.31-1.el8 rhel-baseos 242 k libidn2 x86_64 2.2.0-1.el8 rhel-baseos 94 k libipt x86_64 1.6.1-8.el8 rhel-appstream 50 k libksba x86_64 1.3.5-9.el8_7 rhel-baseos 134 k libmount x86_64 2.32.1-43.el8 rhel-baseos 237 k libmpc x86_64 1.1.0-9.1.el8 rhel-appstream 61 k libnghttp2 x86_64 1.33.0-5.el8_9 rhel-baseos 78 k libnsl2 x86_64 1.2.0-2.20180605git4a062cf.el8 rhel-baseos 58 k libpkgconf x86_64 1.4.2-1.el8 rhel-baseos 35 k libpsl x86_64 0.20.2-6.el8 rhel-baseos 61 k libpwquality x86_64 1.4.4-6.el8 rhel-baseos 107 k libselinux x86_64 2.9-8.el8 rhel-baseos 166 k libsemanage x86_64 2.9-9.el8_6 rhel-baseos 168 k libsepol x86_64 2.9-3.el8 rhel-baseos 340 k libsigsegv x86_64 2.11-5.el8 rhel-baseos 30 k libsmartcols x86_64 2.32.1-43.el8 rhel-baseos 179 k libssh x86_64 0.9.6-13.el8_9 rhel-baseos 220 k libssh-config noarch 0.9.6-13.el8_9 rhel-baseos 21 k libstdc++ x86_64 8.5.0-20.el8 rhel-baseos 455 k libstdc++-devel x86_64 8.5.0-20.el8 rhel-appstream 2.1 M libtasn1 x86_64 4.13-4.el8_7 rhel-baseos 76 k libtirpc x86_64 1.1.4-8.el8 rhel-baseos 113 k libtool-ltdl x86_64 2.4.6-25.el8 rhel-baseos 58 k libunistring x86_64 0.9.9-3.el8 rhel-baseos 422 k libusbx x86_64 1.0.23-4.el8 rhel-baseos 74 k libutempter x86_64 1.1.6-14.el8 rhel-baseos 32 k libuuid x86_64 2.32.1-43.el8 rhel-baseos 99 k libverto x86_64 0.3.2-2.el8 rhel-baseos 24 k libxcrypt x86_64 4.1.1-6.el8 rhel-baseos 73 k libxcrypt-devel x86_64 4.1.1-6.el8 rhel-baseos 25 k libxml2 x86_64 2.9.7-18.el8_9 rhel-baseos 697 k libzstd x86_64 1.4.4-1.el8 rhel-baseos 266 k lua-libs x86_64 5.3.4-12.el8 rhel-baseos 118 k lua-srpm-macros noarch 1-3.el8 epel 8.1 k lz4-libs x86_64 1.8.3-3.el8_4 rhel-baseos 66 k mpfr x86_64 3.1.6-1.el8 rhel-baseos 221 k ncurses x86_64 6.1-10.20180224.el8 rhel-baseos 387 k ncurses-base noarch 6.1-10.20180224.el8 rhel-baseos 81 k ncurses-libs x86_64 6.1-10.20180224.el8 rhel-baseos 334 k nettle x86_64 3.4.1-7.el8 rhel-baseos 301 k npth x86_64 1.5-4.el8 rhel-baseos 26 k ocaml-srpm-macros noarch 5-4.el8 rhel-appstream 9.5 k openblas-srpm-macros noarch 2-2.el8 rhel-appstream 8.0 k openldap x86_64 2.4.46-18.el8 rhel-baseos 352 k openssl-libs x86_64 1:1.1.1k-12.el8_9 rhel-baseos 1.5 M p11-kit x86_64 0.23.22-1.el8 rhel-baseos 324 k p11-kit-trust x86_64 0.23.22-1.el8 rhel-baseos 137 k pam x86_64 1.3.1-27.el8 rhel-baseos 746 k pcre x86_64 8.42-6.el8 rhel-baseos 211 k pcre2 x86_64 10.32-3.el8_6 rhel-baseos 247 k perl-srpm-macros noarch 1-25.el8 rhel-appstream 11 k pkgconf x86_64 1.4.2-1.el8 rhel-baseos 38 k pkgconf-m4 noarch 1.4.2-1.el8 rhel-baseos 17 k pkgconf-pkg-config x86_64 1.4.2-1.el8 rhel-baseos 15 k platform-python x86_64 3.6.8-56.el8_9.3 rhel-baseos 87 k platform-python-setuptools noarch 39.2.0-7.el8 rhel-baseos 632 k popt x86_64 1.18-1.el8 rhel-baseos 61 k publicsuffix-list-dafsa noarch 20180723-1.el8 rhel-baseos 56 k python-rpm-macros noarch 3-45.el8 rhel-appstream 16 k python-srpm-macros noarch 3-45.el8 rhel-appstream 16 k python3-libs x86_64 3.6.8-56.el8_9.3 rhel-baseos 7.8 M python3-pip-wheel noarch 9.0.3-23.el8 rhel-baseos 866 k python3-rpm-macros noarch 3-45.el8 rhel-appstream 15 k python3-setuptools-wheel noarch 39.2.0-7.el8 rhel-baseos 289 k qt5-srpm-macros noarch 5.15.3-1.el8 rhel-appstream 11 k readline x86_64 7.0-10.el8 rhel-baseos 199 k rpm x86_64 4.14.3-28.el8_9 rhel-baseos 544 k rpm-build-libs x86_64 4.14.3-28.el8_9 rhel-baseos 157 k rpm-libs x86_64 4.14.3-28.el8_9 rhel-baseos 348 k rust-srpm-macros noarch 5-2.el8 rhel-appstream 9.3 k setup noarch 2.12.2-9.el8 rhel-baseos 181 k shadow-utils x86_64 2:4.6-19.el8 rhel-baseos 1.2 M sqlite-libs x86_64 3.26.0-19.el8_9 rhel-baseos 581 k systemd-libs x86_64 239-78.el8 rhel-baseos 1.1 M tpm2-tss x86_64 2.3.2-5.el8 rhel-baseos 275 k tzdata noarch 2024a-1.el8 rhel-baseos 475 k xz-libs x86_64 5.2.4-4.el8_6 rhel-baseos 94 k zip x86_64 3.0-23.el8 rhel-baseos 270 k zlib x86_64 1.2.11-25.el8 rhel-baseos 103 k zstd x86_64 1.4.4-1.el8 rhel-appstream 393 k Transaction Summary =========================================================================================== Install 172 Packages Total size: 163 M Installed size: 814 M Downloading Packages: [SKIPPED] cpio-2.13-8.el8.x86_64.rpm: Already downloaded [SKIPPED] bzip2-1.0.6-26.el8.x86_64.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.6-26.el8.x86_64.rpm: Already downloaded [SKIPPED] cracklib-2.9.6-15.el8.x86_64.rpm: Already downloaded [SKIPPED] cracklib-dicts-2.9.6-15.el8.x86_64.rpm: Already downloaded [SKIPPED] grep-3.1-6.el8.x86_64.rpm: Already downloaded [SKIPPED] libassuan-2.5.1-3.el8.x86_64.rpm: Already downloaded [SKIPPED] libattr-2.4.48-3.el8.x86_64.rpm: Already downloaded [SKIPPED] libsigsegv-2.11-5.el8.x86_64.rpm: Already downloaded [SKIPPED] libunistring-0.9.9-3.el8.x86_64.rpm: Already downloaded [SKIPPED] libutempter-1.1.6-14.el8.x86_64.rpm: Already downloaded [SKIPPED] mpfr-3.1.6-1.el8.x86_64.rpm: Already downloaded 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gdb-headless-8.2-20.el8.x86_64.rpm: Already downloaded [SKIPPED] libstdc++-devel-8.5.0-20.el8.x86_64.rpm: Already downloaded [SKIPPED] rpm-build-4.14.3-28.el8_9.x86_64.rpm: Already downloaded [SKIPPED] ansible-srpm-macros-1-12.el8.noarch.rpm: Already downloaded [SKIPPED] epel-rpm-macros-8-41.noarch.rpm: Already downloaded [SKIPPED] fpc-srpm-macros-1.3-1.el8.noarch.rpm: Already downloaded [SKIPPED] lua-srpm-macros-1-3.el8.noarch.rpm: Already downloaded Red Hat Enterprise Linux - BaseOS 3.1 MB/s | 3.1 kB 00:00 Importing GPG key 0xFD431D51: Userid : "Red Hat, Inc. (release key 2) " Fingerprint: 567E 347A D004 4ADE 55BA 8A5F 199E 2F91 FD43 1D51 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat8-release Key imported successfully Importing GPG key 0x2FA658E0: Userid : "Red Hat, Inc. (auxiliary key) " Fingerprint: 43A6 E49C 4A38 F4BE 9ABF 2A53 4568 9C88 2FA6 58E0 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat8-release Key imported successfully Extra Packages for Enterprise Linux 8 - x86_64 1.6 MB/s | 1.6 kB 00:00 Key imported successfullyImporting GPG key 0x2F86D6A1: Userid : "Fedora EPEL (8) " Fingerprint: 94E2 79EB 8D8F 25B2 1810 ADF1 21EA 45AB 2F86 D6A1 From : /usr/share/distribution-gpg-keys/epel/RPM-GPG-KEY-EPEL-8 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.8-6.el8.x86_64 1/1 Preparing : 1/1 Installing : libgcc-8.5.0-20.el8.x86_64 1/172 Running scriptlet: libgcc-8.5.0-20.el8.x86_64 1/172 Installing : python-srpm-macros-3-45.el8.noarch 2/172 Installing : crypto-policies-20230731-1.git3177e06.el8.noarch 3/172 Running scriptlet: crypto-policies-20230731-1.git3177e06.el8.noarch 3/172 Installing : python-rpm-macros-3-45.el8.noarch 4/172 Installing : redhat-release-8.9-0.1.el8.x86_64 5/172 Installing : setup-2.12.2-9.el8.noarch 6/172 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.12.2-9.el8.noarch 6/172 Installing : filesystem-3.8-6.el8.x86_64 7/172 Installing : python3-pip-wheel-9.0.3-23.el8.noarch 8/172 Installing : python3-setuptools-wheel-39.2.0-7.el8.noarch 9/172 Installing : basesystem-11-5.el8.noarch 10/172 Installing : python3-rpm-macros-3-45.el8.noarch 11/172 Installing : fpc-srpm-macros-1.3-1.el8.noarch 12/172 Installing : ansible-srpm-macros-1-12.el8.noarch 13/172 Installing : qt5-srpm-macros-5.15.3-1.el8.noarch 14/172 Installing : go-srpm-macros-2-17.el8.noarch 15/172 Installing : rust-srpm-macros-5-2.el8.noarch 16/172 Installing : perl-srpm-macros-1-25.el8.noarch 17/172 Installing : openblas-srpm-macros-2-2.el8.noarch 18/172 Installing : ocaml-srpm-macros-5-4.el8.noarch 19/172 Installing : ghc-srpm-macros-1.4.2-7.el8.noarch 20/172 Installing : kernel-headers-4.18.0-513.18.1.el8_9.x86_64 21/172 Installing : tzdata-2024a-1.el8.noarch 22/172 Installing : libssh-config-0.9.6-13.el8_9.noarch 23/172 Installing : ncurses-base-6.1-10.20180224.el8.noarch 24/172 Installing : pcre2-10.32-3.el8_6.x86_64 25/172 Installing : libselinux-2.9-8.el8.x86_64 26/172 Installing : ncurses-libs-6.1-10.20180224.el8.x86_64 27/172 Installing : glibc-all-langpacks-2.28-236.el8_9.12.x86_64 28/172 Installing : glibc-common-2.28-236.el8_9.12.x86_64 29/172 Installing : glibc-gconv-extra-2.28-236.el8_9.12.x86_64 30/172 Running 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mpfr-3.1.6-1.el8.x86_64 43/172 Running scriptlet: mpfr-3.1.6-1.el8.x86_64 43/172 Installing : readline-7.0-10.el8.x86_64 44/172 Running scriptlet: readline-7.0-10.el8.x86_64 44/172 Installing : sqlite-libs-3.26.0-19.el8_9.x86_64 45/172 Installing : popt-1.18-1.el8.x86_64 46/172 Installing : libcap-2.48-6.el8_9.x86_64 47/172 Installing : libcom_err-1.45.6-5.el8.x86_64 48/172 Running scriptlet: libcom_err-1.45.6-5.el8.x86_64 48/172 Installing : libuuid-2.32.1-43.el8.x86_64 49/172 Running scriptlet: libuuid-2.32.1-43.el8.x86_64 49/172 Installing : chkconfig-1.19.2-1.el8.x86_64 50/172 Installing : libunistring-0.9.9-3.el8.x86_64 51/172 Installing : libattr-2.4.48-3.el8.x86_64 52/172 Installing : libacl-2.2.53-1.el8.x86_64 53/172 Installing : sed-4.5-5.el8.x86_64 54/172 Running scriptlet: sed-4.5-5.el8.x86_64 54/172 Installing : libgpg-error-1.31-1.el8.x86_64 55/172 Installing : lua-libs-5.3.4-12.el8.x86_64 56/172 Installing : libffi-3.1-24.el8.x86_64 57/172 Installing : p11-kit-0.23.22-1.el8.x86_64 58/172 Installing : libidn2-2.2.0-1.el8.x86_64 59/172 Installing : libmpc-1.1.0-9.1.el8.x86_64 60/172 Installing : file-libs-5.33-25.el8.x86_64 61/172 Installing : file-5.33-25.el8.x86_64 62/172 Installing : libgcrypt-1.8.5-7.el8_6.x86_64 63/172 Running scriptlet: libgcrypt-1.8.5-7.el8_6.x86_64 63/172 Installing : unzip-6.0-46.el8.x86_64 64/172 Installing : findutils-1:4.6.0-21.el8.x86_64 65/172 Running scriptlet: findutils-1:4.6.0-21.el8.x86_64 65/172 Installing : elfutils-default-yama-scope-0.189-3.el8.noarch 66/172 Running scriptlet: elfutils-default-yama-scope-0.189-3.el8.noarch 66/172 Installing : elfutils-libs-0.189-3.el8.x86_64 67/172 Running scriptlet: glibc-headers-2.28-236.el8_9.12.x86_64 68/172 Installing : glibc-headers-2.28-236.el8_9.12.x86_64 68/172 Installing : lz4-libs-1.8.3-3.el8_4.x86_64 69/172 Installing : libcap-ng-0.7.11-1.el8.x86_64 70/172 Installing : audit-libs-3.0.7-5.el8.x86_64 71/172 Installing : pcre-8.42-6.el8.x86_64 72/172 Installing : grep-3.1-6.el8.x86_64 73/172 Running scriptlet: grep-3.1-6.el8.x86_64 73/172 Installing : keyutils-libs-1.5.10-9.el8.x86_64 74/172 Installing : gdbm-libs-1:1.18-2.el8.x86_64 75/172 Installing : libtasn1-4.13-4.el8_7.x86_64 76/172 Running scriptlet: libtasn1-4.13-4.el8_7.x86_64 76/172 Installing : p11-kit-trust-0.23.22-1.el8.x86_64 77/172 Running scriptlet: p11-kit-trust-0.23.22-1.el8.x86_64 77/172 Installing : expat-2.2.5-11.el8.x86_64 78/172 Installing : gdbm-1:1.18-2.el8.x86_64 79/172 Installing : xz-5.2.4-4.el8_6.x86_64 80/172 Installing : libsemanage-2.9-9.el8_6.x86_64 81/172 Installing : elfutils-0.189-3.el8.x86_64 82/172 Installing : zip-3.0-23.el8.x86_64 83/172 Installing : cpp-8.5.0-20.el8.x86_64 84/172 Running scriptlet: cpp-8.5.0-20.el8.x86_64 84/172 Installing : libassuan-2.5.1-3.el8.x86_64 85/172 Installing : libksba-1.3.5-9.el8_7.x86_64 86/172 Installing : tar-2:1.30-9.el8.x86_64 87/172 Running scriptlet: tar-2:1.30-9.el8.x86_64 87/172 Installing : patch-2.7.6-11.el8.x86_64 88/172 Installing : dwz-0.12-10.el8.x86_64 89/172 Installing : zstd-1.4.4-1.el8.x86_64 90/172 Installing : libstdc++-devel-8.5.0-20.el8.x86_64 91/172 Installing : nettle-3.4.1-7.el8.x86_64 92/172 Running scriptlet: nettle-3.4.1-7.el8.x86_64 92/172 Installing : gnutls-3.6.16-8.el8_9.1.x86_64 93/172 Installing : isl-0.16.1-6.el8.x86_64 94/172 Running scriptlet: isl-0.16.1-6.el8.x86_64 94/172 Installing : libxml2-2.9.7-18.el8_9.x86_64 95/172 Installing : bzip2-1.0.6-26.el8.x86_64 96/172 Installing : diffutils-3.6-6.el8.x86_64 97/172 Running scriptlet: diffutils-3.6-6.el8.x86_64 97/172 Installing : coreutils-common-8.30-15.el8.x86_64 98/172 Running scriptlet: coreutils-common-8.30-15.el8.x86_64 98/172 Installing : libgomp-8.5.0-20.el8.x86_64 99/172 Running scriptlet: libgomp-8.5.0-20.el8.x86_64 99/172 Installing : cpio-2.13-8.el8.x86_64 100/172 Installing : libsigsegv-2.11-5.el8.x86_64 101/172 Installing : gawk-4.2.1-4.el8.x86_64 102/172 Installing : 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libdb-5.3.28-42.el8_4.x86_64 115/172 Running scriptlet: libdb-5.3.28-42.el8_4.x86_64 115/172 Installing : krb5-libs-1.18.2-26.el8_9.x86_64 116/172 Installing : libtirpc-1.1.4-8.el8.x86_64 117/172 Running scriptlet: libtirpc-1.1.4-8.el8.x86_64 117/172 Installing : libblkid-2.32.1-43.el8.x86_64 118/172 Running scriptlet: libblkid-2.32.1-43.el8.x86_64 118/172 Installing : libmount-2.32.1-43.el8.x86_64 119/172 Running scriptlet: libmount-2.32.1-43.el8.x86_64 119/172 Installing : systemd-libs-239-78.el8.x86_64 120/172 Running scriptlet: systemd-libs-239-78.el8.x86_64 120/172 Installing : libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 121/172 Running scriptlet: libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 121/172 Installing : platform-python-setuptools-39.2.0-7.el8.noarch 122/172 Installing : platform-python-3.6.8-56.el8_9.3.x86_64 123/172 Running scriptlet: platform-python-3.6.8-56.el8_9.3.x86_64 123/172 Installing : python3-libs-3.6.8-56.el8_9.3.x86_64 124/172 Installing : gzip-1.9-13.el8_5.x86_64 125/172 Running scriptlet: gzip-1.9-13.el8_5.x86_64 125/172 Installing : cracklib-2.9.6-15.el8.x86_64 126/172 Installing : cracklib-dicts-2.9.6-15.el8.x86_64 127/172 Installing : binutils-2.30-123.el8.x86_64 128/172 Running scriptlet: binutils-2.30-123.el8.x86_64 128/172 Installing : shadow-utils-2:4.6-19.el8.x86_64 129/172 Running scriptlet: libutempter-1.1.6-14.el8.x86_64 130/172 Installing : libutempter-1.1.6-14.el8.x86_64 130/172 Running scriptlet: tpm2-tss-2.3.2-5.el8.x86_64 131/172 Installing : tpm2-tss-2.3.2-5.el8.x86_64 131/172 Running scriptlet: tpm2-tss-2.3.2-5.el8.x86_64 131/172 Installing : ima-evm-utils-1.3.2-12.el8.x86_64 132/172 Installing : libpwquality-1.4.4-6.el8.x86_64 133/172 Installing : pam-1.3.1-27.el8.x86_64 134/172 Running scriptlet: pam-1.3.1-27.el8.x86_64 134/172 Installing : libusbx-1.0.23-4.el8.x86_64 135/172 Installing : glib2-2.56.4-161.el8.x86_64 136/172 Installing : libbabeltrace-1.5.4-4.el8.x86_64 137/172 Running scriptlet: libbabeltrace-1.5.4-4.el8.x86_64 137/172 Installing : libfdisk-2.32.1-43.el8.x86_64 138/172 Running scriptlet: libfdisk-2.32.1-43.el8.x86_64 138/172 Installing : cyrus-sasl-lib-2.1.27-6.el8_5.x86_64 139/172 Running scriptlet: cyrus-sasl-lib-2.1.27-6.el8_5.x86_64 139/172 Installing : openldap-2.4.46-18.el8.x86_64 140/172 Installing : gnupg2-2.2.20-3.el8_6.x86_64 141/172 Installing : libssh-0.9.6-13.el8_9.x86_64 142/172 Installing : libdb-utils-5.3.28-42.el8_4.x86_64 143/172 Installing : libarchive-3.3.3-5.el8.x86_64 144/172 Installing : libatomic_ops-7.6.2-3.el8.x86_64 145/172 Installing : gc-7.6.4-3.el8.x86_64 146/172 Installing : guile-5:2.0.14-7.el8.x86_64 147/172 Running scriptlet: guile-5:2.0.14-7.el8.x86_64 147/172 Installing : libipt-1.6.1-8.el8.x86_64 148/172 Installing : publicsuffix-list-dafsa-20180723-1.el8.noarch 149/172 Installing : libpsl-0.20.2-6.el8.x86_64 150/172 Installing : libcurl-7.61.1-33.el8.x86_64 151/172 Installing : curl-7.61.1-33.el8.x86_64 152/172 Installing 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redhat-rpm-config-131-1.el8.noarch 166/172 Installing : rpm-build-4.14.3-28.el8_9.x86_64 167/172 Installing : gcc-c++-8.5.0-20.el8.x86_64 168/172 Installing : epel-rpm-macros-8-41.noarch 169/172 Installing : util-linux-2.32.1-43.el8.x86_64 170/172 Running scriptlet: util-linux-2.32.1-43.el8.x86_64 170/172 Installing : which-2.21-20.el8.x86_64 171/172 Installing : make-1:4.2.1-11.el8.x86_64 172/172 Running scriptlet: make-1:4.2.1-11.el8.x86_64 172/172 Running scriptlet: filesystem-3.8-6.el8.x86_64 172/172 Running scriptlet: glibc-all-langpacks-2.28-236.el8_9.12.x86_64 172/172 Running scriptlet: ca-certificates-2023.2.60_v7.0.306-80.0.el8_8.no 172/172 Running scriptlet: guile-5:2.0.14-7.el8.x86_64 172/172 Running scriptlet: make-1:4.2.1-11.el8.x86_64 172/172 Verifying : cpio-2.13-8.el8.x86_64 1/172 Verifying : bzip2-1.0.6-26.el8.x86_64 2/172 Verifying : bzip2-libs-1.0.6-26.el8.x86_64 3/172 Verifying : cracklib-2.9.6-15.el8.x86_64 4/172 Verifying : cracklib-dicts-2.9.6-15.el8.x86_64 5/172 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gmp-1:6.1.2-10.el8.x86_64 26/172 Verifying : diffutils-3.6-6.el8.x86_64 27/172 Verifying : libidn2-2.2.0-1.el8.x86_64 28/172 Verifying : patch-2.7.6-11.el8.x86_64 29/172 Verifying : libusbx-1.0.23-4.el8.x86_64 30/172 Verifying : libzstd-1.4.4-1.el8.x86_64 31/172 Verifying : libpsl-0.20.2-6.el8.x86_64 32/172 Verifying : p11-kit-trust-0.23.22-1.el8.x86_64 33/172 Verifying : popt-1.18-1.el8.x86_64 34/172 Verifying : brotli-1.0.6-3.el8.x86_64 35/172 Verifying : ima-evm-utils-1.3.2-12.el8.x86_64 36/172 Verifying : lz4-libs-1.8.3-3.el8_4.x86_64 37/172 Verifying : p11-kit-0.23.22-1.el8.x86_64 38/172 Verifying : filesystem-3.8-6.el8.x86_64 39/172 Verifying : libcap-ng-0.7.11-1.el8.x86_64 40/172 Verifying : libdb-5.3.28-42.el8_4.x86_64 41/172 Verifying : libdb-utils-5.3.28-42.el8_4.x86_64 42/172 Verifying : libxcrypt-4.1.1-6.el8.x86_64 43/172 Verifying : libxcrypt-devel-4.1.1-6.el8.x86_64 44/172 Verifying : nettle-3.4.1-7.el8.x86_64 45/172 Verifying : openldap-2.4.46-18.el8.x86_64 46/172 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libverto-0.3.2-2.el8.x86_64 68/172 Verifying : pcre2-10.32-3.el8_6.x86_64 69/172 Verifying : gdbm-1:1.18-2.el8.x86_64 70/172 Verifying : libksba-1.3.5-9.el8_7.x86_64 71/172 Verifying : libtasn1-4.13-4.el8_7.x86_64 72/172 Verifying : coreutils-8.30-15.el8.x86_64 73/172 Verifying : coreutils-common-8.30-15.el8.x86_64 74/172 Verifying : expat-2.2.5-11.el8.x86_64 75/172 Verifying : glib2-2.56.4-161.el8.x86_64 76/172 Verifying : libarchive-3.3.3-5.el8.x86_64 77/172 Verifying : libffi-3.1-24.el8.x86_64 78/172 Verifying : libpwquality-1.4.4-6.el8.x86_64 79/172 Verifying : libselinux-2.9-8.el8.x86_64 80/172 Verifying : platform-python-setuptools-39.2.0-7.el8.noarch 81/172 Verifying : python3-setuptools-wheel-39.2.0-7.el8.noarch 82/172 Verifying : setup-2.12.2-9.el8.noarch 83/172 Verifying : tar-2:1.30-9.el8.x86_64 84/172 Verifying : audit-libs-3.0.7-5.el8.x86_64 85/172 Verifying : binutils-2.30-123.el8.x86_64 86/172 Verifying : ca-certificates-2023.2.60_v7.0.306-80.0.el8_8.no 87/172 Verifying : chkconfig-1.19.2-1.el8.x86_64 88/172 Verifying : crypto-policies-20230731-1.git3177e06.el8.noarch 89/172 Verifying : curl-7.61.1-33.el8.x86_64 90/172 Verifying : elfutils-0.189-3.el8.x86_64 91/172 Verifying : elfutils-libelf-0.189-3.el8.x86_64 92/172 Verifying : elfutils-libs-0.189-3.el8.x86_64 93/172 Verifying : file-5.33-25.el8.x86_64 94/172 Verifying : file-libs-5.33-25.el8.x86_64 95/172 Verifying : findutils-1:4.6.0-21.el8.x86_64 96/172 Verifying : libcurl-7.61.1-33.el8.x86_64 97/172 Verifying : libgcc-8.5.0-20.el8.x86_64 98/172 Verifying : libgomp-8.5.0-20.el8.x86_64 99/172 Verifying : libmount-2.32.1-43.el8.x86_64 100/172 Verifying : libnghttp2-1.33.0-5.el8_9.x86_64 101/172 Verifying : libsmartcols-2.32.1-43.el8.x86_64 102/172 Verifying : libstdc++-8.5.0-20.el8.x86_64 103/172 Verifying : libuuid-2.32.1-43.el8.x86_64 104/172 Verifying : ncurses-libs-6.1-10.20180224.el8.x86_64 105/172 Verifying : pam-1.3.1-27.el8.x86_64 106/172 Verifying : util-linux-2.32.1-43.el8.x86_64 107/172 Verifying : which-2.21-20.el8.x86_64 108/172 Verifying : elfutils-default-yama-scope-0.189-3.el8.noarch 109/172 Verifying : krb5-libs-1.18.2-26.el8_9.x86_64 110/172 Verifying : libblkid-2.32.1-43.el8.x86_64 111/172 Verifying : libcap-2.48-6.el8_9.x86_64 112/172 Verifying : libfdisk-2.32.1-43.el8.x86_64 113/172 Verifying : libxml2-2.9.7-18.el8_9.x86_64 114/172 Verifying : ncurses-6.1-10.20180224.el8.x86_64 115/172 Verifying : ncurses-base-6.1-10.20180224.el8.noarch 116/172 Verifying : openssl-libs-1:1.1.1k-12.el8_9.x86_64 117/172 Verifying : platform-python-3.6.8-56.el8_9.3.x86_64 118/172 Verifying : python3-libs-3.6.8-56.el8_9.3.x86_64 119/172 Verifying : python3-pip-wheel-9.0.3-23.el8.noarch 120/172 Verifying : redhat-release-8.9-0.1.el8.x86_64 121/172 Verifying : shadow-utils-2:4.6-19.el8.x86_64 122/172 Verifying : sqlite-libs-3.26.0-19.el8_9.x86_64 123/172 Verifying : systemd-libs-239-78.el8.x86_64 124/172 Verifying : tpm2-tss-2.3.2-5.el8.x86_64 125/172 Verifying : zlib-1.2.11-25.el8.x86_64 126/172 Verifying : gnutls-3.6.16-8.el8_9.1.x86_64 127/172 Verifying : libssh-0.9.6-13.el8_9.x86_64 128/172 Verifying : libssh-config-0.9.6-13.el8_9.noarch 129/172 Verifying : rpm-4.14.3-28.el8_9.x86_64 130/172 Verifying : rpm-build-libs-4.14.3-28.el8_9.x86_64 131/172 Verifying : rpm-libs-4.14.3-28.el8_9.x86_64 132/172 Verifying : tzdata-2024a-1.el8.noarch 133/172 Verifying : glibc-2.28-236.el8_9.12.x86_64 134/172 Verifying : glibc-all-langpacks-2.28-236.el8_9.12.x86_64 135/172 Verifying : glibc-common-2.28-236.el8_9.12.x86_64 136/172 Verifying : glibc-devel-2.28-236.el8_9.12.x86_64 137/172 Verifying : glibc-gconv-extra-2.28-236.el8_9.12.x86_64 138/172 Verifying : glibc-headers-2.28-236.el8_9.12.x86_64 139/172 Verifying : kernel-headers-4.18.0-513.18.1.el8_9.x86_64 140/172 Verifying : ghc-srpm-macros-1.4.2-7.el8.noarch 141/172 Verifying : ocaml-srpm-macros-5-4.el8.noarch 142/172 Verifying : openblas-srpm-macros-2-2.el8.noarch 143/172 Verifying : perl-srpm-macros-1-25.el8.noarch 144/172 Verifying : rust-srpm-macros-5-2.el8.noarch 145/172 Verifying : libatomic_ops-7.6.2-3.el8.x86_64 146/172 Verifying : gc-7.6.4-3.el8.x86_64 147/172 Verifying : guile-5:2.0.14-7.el8.x86_64 148/172 Verifying : isl-0.16.1-6.el8.x86_64 149/172 Verifying : libipt-1.6.1-8.el8.x86_64 150/172 Verifying : zstd-1.4.4-1.el8.x86_64 151/172 Verifying : libmpc-1.1.0-9.1.el8.x86_64 152/172 Verifying : efi-srpm-macros-3-3.el8.noarch 153/172 Verifying : go-srpm-macros-2-17.el8.noarch 154/172 Verifying : dwz-0.12-10.el8.x86_64 155/172 Verifying : qt5-srpm-macros-5.15.3-1.el8.noarch 156/172 Verifying : python-rpm-macros-3-45.el8.noarch 157/172 Verifying : python3-rpm-macros-3-45.el8.noarch 158/172 Verifying : redhat-rpm-config-131-1.el8.noarch 159/172 Verifying : python-srpm-macros-3-45.el8.noarch 160/172 Verifying : gcc-c++-8.5.0-20.el8.x86_64 161/172 Verifying : gcc-plugin-annobin-8.5.0-20.el8.x86_64 162/172 Verifying : annobin-11.13-2.el8.x86_64 163/172 Verifying : cpp-8.5.0-20.el8.x86_64 164/172 Verifying : gcc-8.5.0-20.el8.x86_64 165/172 Verifying : gdb-headless-8.2-20.el8.x86_64 166/172 Verifying : libstdc++-devel-8.5.0-20.el8.x86_64 167/172 Verifying : rpm-build-4.14.3-28.el8_9.x86_64 168/172 Verifying : ansible-srpm-macros-1-12.el8.noarch 169/172 Verifying : epel-rpm-macros-8-41.noarch 170/172 Verifying : fpc-srpm-macros-1.3-1.el8.noarch 171/172 Verifying : lua-srpm-macros-1-3.el8.noarch 172/172 Installed products updated. Installed: annobin-11.13-2.el8.x86_64 ansible-srpm-macros-1-12.el8.noarch audit-libs-3.0.7-5.el8.x86_64 basesystem-11-5.el8.noarch bash-4.4.20-4.el8_6.x86_64 binutils-2.30-123.el8.x86_64 brotli-1.0.6-3.el8.x86_64 bzip2-1.0.6-26.el8.x86_64 bzip2-libs-1.0.6-26.el8.x86_64 ca-certificates-2023.2.60_v7.0.306-80.0.el8_8.noarch chkconfig-1.19.2-1.el8.x86_64 coreutils-8.30-15.el8.x86_64 coreutils-common-8.30-15.el8.x86_64 cpio-2.13-8.el8.x86_64 cpp-8.5.0-20.el8.x86_64 cracklib-2.9.6-15.el8.x86_64 cracklib-dicts-2.9.6-15.el8.x86_64 crypto-policies-20230731-1.git3177e06.el8.noarch curl-7.61.1-33.el8.x86_64 cyrus-sasl-lib-2.1.27-6.el8_5.x86_64 diffutils-3.6-6.el8.x86_64 dwz-0.12-10.el8.x86_64 efi-srpm-macros-3-3.el8.noarch elfutils-0.189-3.el8.x86_64 elfutils-default-yama-scope-0.189-3.el8.noarch elfutils-libelf-0.189-3.el8.x86_64 elfutils-libs-0.189-3.el8.x86_64 epel-rpm-macros-8-41.noarch expat-2.2.5-11.el8.x86_64 file-5.33-25.el8.x86_64 file-libs-5.33-25.el8.x86_64 filesystem-3.8-6.el8.x86_64 findutils-1:4.6.0-21.el8.x86_64 fpc-srpm-macros-1.3-1.el8.noarch gawk-4.2.1-4.el8.x86_64 gc-7.6.4-3.el8.x86_64 gcc-8.5.0-20.el8.x86_64 gcc-c++-8.5.0-20.el8.x86_64 gcc-plugin-annobin-8.5.0-20.el8.x86_64 gdb-headless-8.2-20.el8.x86_64 gdbm-1:1.18-2.el8.x86_64 gdbm-libs-1:1.18-2.el8.x86_64 ghc-srpm-macros-1.4.2-7.el8.noarch glib2-2.56.4-161.el8.x86_64 glibc-2.28-236.el8_9.12.x86_64 glibc-all-langpacks-2.28-236.el8_9.12.x86_64 glibc-common-2.28-236.el8_9.12.x86_64 glibc-devel-2.28-236.el8_9.12.x86_64 glibc-gconv-extra-2.28-236.el8_9.12.x86_64 glibc-headers-2.28-236.el8_9.12.x86_64 gmp-1:6.1.2-10.el8.x86_64 gnupg2-2.2.20-3.el8_6.x86_64 gnutls-3.6.16-8.el8_9.1.x86_64 go-srpm-macros-2-17.el8.noarch grep-3.1-6.el8.x86_64 guile-5:2.0.14-7.el8.x86_64 gzip-1.9-13.el8_5.x86_64 ima-evm-utils-1.3.2-12.el8.x86_64 info-6.5-7.el8.x86_64 isl-0.16.1-6.el8.x86_64 kernel-headers-4.18.0-513.18.1.el8_9.x86_64 keyutils-libs-1.5.10-9.el8.x86_64 krb5-libs-1.18.2-26.el8_9.x86_64 libacl-2.2.53-1.el8.x86_64 libarchive-3.3.3-5.el8.x86_64 libassuan-2.5.1-3.el8.x86_64 libatomic_ops-7.6.2-3.el8.x86_64 libattr-2.4.48-3.el8.x86_64 libbabeltrace-1.5.4-4.el8.x86_64 libblkid-2.32.1-43.el8.x86_64 libcap-2.48-6.el8_9.x86_64 libcap-ng-0.7.11-1.el8.x86_64 libcom_err-1.45.6-5.el8.x86_64 libcurl-7.61.1-33.el8.x86_64 libdb-5.3.28-42.el8_4.x86_64 libdb-utils-5.3.28-42.el8_4.x86_64 libfdisk-2.32.1-43.el8.x86_64 libffi-3.1-24.el8.x86_64 libgcc-8.5.0-20.el8.x86_64 libgcrypt-1.8.5-7.el8_6.x86_64 libgomp-8.5.0-20.el8.x86_64 libgpg-error-1.31-1.el8.x86_64 libidn2-2.2.0-1.el8.x86_64 libipt-1.6.1-8.el8.x86_64 libksba-1.3.5-9.el8_7.x86_64 libmount-2.32.1-43.el8.x86_64 libmpc-1.1.0-9.1.el8.x86_64 libnghttp2-1.33.0-5.el8_9.x86_64 libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 libpkgconf-1.4.2-1.el8.x86_64 libpsl-0.20.2-6.el8.x86_64 libpwquality-1.4.4-6.el8.x86_64 libselinux-2.9-8.el8.x86_64 libsemanage-2.9-9.el8_6.x86_64 libsepol-2.9-3.el8.x86_64 libsigsegv-2.11-5.el8.x86_64 libsmartcols-2.32.1-43.el8.x86_64 libssh-0.9.6-13.el8_9.x86_64 libssh-config-0.9.6-13.el8_9.noarch libstdc++-8.5.0-20.el8.x86_64 libstdc++-devel-8.5.0-20.el8.x86_64 libtasn1-4.13-4.el8_7.x86_64 libtirpc-1.1.4-8.el8.x86_64 libtool-ltdl-2.4.6-25.el8.x86_64 libunistring-0.9.9-3.el8.x86_64 libusbx-1.0.23-4.el8.x86_64 libutempter-1.1.6-14.el8.x86_64 libuuid-2.32.1-43.el8.x86_64 libverto-0.3.2-2.el8.x86_64 libxcrypt-4.1.1-6.el8.x86_64 libxcrypt-devel-4.1.1-6.el8.x86_64 libxml2-2.9.7-18.el8_9.x86_64 libzstd-1.4.4-1.el8.x86_64 lua-libs-5.3.4-12.el8.x86_64 lua-srpm-macros-1-3.el8.noarch lz4-libs-1.8.3-3.el8_4.x86_64 make-1:4.2.1-11.el8.x86_64 mpfr-3.1.6-1.el8.x86_64 ncurses-6.1-10.20180224.el8.x86_64 ncurses-base-6.1-10.20180224.el8.noarch ncurses-libs-6.1-10.20180224.el8.x86_64 nettle-3.4.1-7.el8.x86_64 npth-1.5-4.el8.x86_64 ocaml-srpm-macros-5-4.el8.noarch openblas-srpm-macros-2-2.el8.noarch openldap-2.4.46-18.el8.x86_64 openssl-libs-1:1.1.1k-12.el8_9.x86_64 p11-kit-0.23.22-1.el8.x86_64 p11-kit-trust-0.23.22-1.el8.x86_64 pam-1.3.1-27.el8.x86_64 patch-2.7.6-11.el8.x86_64 pcre-8.42-6.el8.x86_64 pcre2-10.32-3.el8_6.x86_64 perl-srpm-macros-1-25.el8.noarch pkgconf-1.4.2-1.el8.x86_64 pkgconf-m4-1.4.2-1.el8.noarch pkgconf-pkg-config-1.4.2-1.el8.x86_64 platform-python-3.6.8-56.el8_9.3.x86_64 platform-python-setuptools-39.2.0-7.el8.noarch popt-1.18-1.el8.x86_64 publicsuffix-list-dafsa-20180723-1.el8.noarch python-rpm-macros-3-45.el8.noarch python-srpm-macros-3-45.el8.noarch python3-libs-3.6.8-56.el8_9.3.x86_64 python3-pip-wheel-9.0.3-23.el8.noarch python3-rpm-macros-3-45.el8.noarch python3-setuptools-wheel-39.2.0-7.el8.noarch qt5-srpm-macros-5.15.3-1.el8.noarch readline-7.0-10.el8.x86_64 redhat-release-8.9-0.1.el8.x86_64 redhat-rpm-config-131-1.el8.noarch rpm-4.14.3-28.el8_9.x86_64 rpm-build-4.14.3-28.el8_9.x86_64 rpm-build-libs-4.14.3-28.el8_9.x86_64 rpm-libs-4.14.3-28.el8_9.x86_64 rust-srpm-macros-5-2.el8.noarch sed-4.5-5.el8.x86_64 setup-2.12.2-9.el8.noarch shadow-utils-2:4.6-19.el8.x86_64 sqlite-libs-3.26.0-19.el8_9.x86_64 systemd-libs-239-78.el8.x86_64 tar-2:1.30-9.el8.x86_64 tpm2-tss-2.3.2-5.el8.x86_64 tzdata-2024a-1.el8.noarch unzip-6.0-46.el8.x86_64 util-linux-2.32.1-43.el8.x86_64 which-2.21-20.el8.x86_64 xz-5.2.4-4.el8_6.x86_64 xz-libs-5.2.4-4.el8_6.x86_64 zip-3.0-23.el8.x86_64 zlib-1.2.11-25.el8.x86_64 zstd-1.4.4-1.el8.x86_64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: annobin-11.13-2.el8.x86_64 ansible-srpm-macros-1-12.el8.noarch audit-libs-3.0.7-5.el8.x86_64 basesystem-11-5.el8.noarch bash-4.4.20-4.el8_6.x86_64 binutils-2.30-123.el8.x86_64 brotli-1.0.6-3.el8.x86_64 bzip2-1.0.6-26.el8.x86_64 bzip2-libs-1.0.6-26.el8.x86_64 ca-certificates-2023.2.60_v7.0.306-80.0.el8_8.noarch chkconfig-1.19.2-1.el8.x86_64 coreutils-8.30-15.el8.x86_64 coreutils-common-8.30-15.el8.x86_64 cpio-2.13-8.el8.x86_64 cpp-8.5.0-20.el8.x86_64 cracklib-2.9.6-15.el8.x86_64 cracklib-dicts-2.9.6-15.el8.x86_64 crypto-policies-20230731-1.git3177e06.el8.noarch curl-7.61.1-33.el8.x86_64 cyrus-sasl-lib-2.1.27-6.el8_5.x86_64 diffutils-3.6-6.el8.x86_64 dwz-0.12-10.el8.x86_64 efi-srpm-macros-3-3.el8.noarch elfutils-0.189-3.el8.x86_64 elfutils-default-yama-scope-0.189-3.el8.noarch elfutils-libelf-0.189-3.el8.x86_64 elfutils-libs-0.189-3.el8.x86_64 epel-rpm-macros-8-41.noarch expat-2.2.5-11.el8.x86_64 file-5.33-25.el8.x86_64 file-libs-5.33-25.el8.x86_64 filesystem-3.8-6.el8.x86_64 findutils-4.6.0-21.el8.x86_64 fpc-srpm-macros-1.3-1.el8.noarch gawk-4.2.1-4.el8.x86_64 gc-7.6.4-3.el8.x86_64 gcc-8.5.0-20.el8.x86_64 gcc-c++-8.5.0-20.el8.x86_64 gcc-plugin-annobin-8.5.0-20.el8.x86_64 gdb-headless-8.2-20.el8.x86_64 gdbm-1.18-2.el8.x86_64 gdbm-libs-1.18-2.el8.x86_64 ghc-srpm-macros-1.4.2-7.el8.noarch glib2-2.56.4-161.el8.x86_64 glibc-2.28-236.el8_9.12.x86_64 glibc-all-langpacks-2.28-236.el8_9.12.x86_64 glibc-common-2.28-236.el8_9.12.x86_64 glibc-devel-2.28-236.el8_9.12.x86_64 glibc-gconv-extra-2.28-236.el8_9.12.x86_64 glibc-headers-2.28-236.el8_9.12.x86_64 gmp-6.1.2-10.el8.x86_64 gnupg2-2.2.20-3.el8_6.x86_64 gnutls-3.6.16-8.el8_9.1.x86_64 go-srpm-macros-2-17.el8.noarch gpg-pubkey-2f86d6a1-5cf7cefb gpg-pubkey-2fa658e0-45700c69 gpg-pubkey-fd431d51-4ae0493b grep-3.1-6.el8.x86_64 guile-2.0.14-7.el8.x86_64 gzip-1.9-13.el8_5.x86_64 ima-evm-utils-1.3.2-12.el8.x86_64 info-6.5-7.el8.x86_64 isl-0.16.1-6.el8.x86_64 kernel-headers-4.18.0-513.18.1.el8_9.x86_64 keyutils-libs-1.5.10-9.el8.x86_64 krb5-libs-1.18.2-26.el8_9.x86_64 libacl-2.2.53-1.el8.x86_64 libarchive-3.3.3-5.el8.x86_64 libassuan-2.5.1-3.el8.x86_64 libatomic_ops-7.6.2-3.el8.x86_64 libattr-2.4.48-3.el8.x86_64 libbabeltrace-1.5.4-4.el8.x86_64 libblkid-2.32.1-43.el8.x86_64 libcap-2.48-6.el8_9.x86_64 libcap-ng-0.7.11-1.el8.x86_64 libcom_err-1.45.6-5.el8.x86_64 libcurl-7.61.1-33.el8.x86_64 libdb-5.3.28-42.el8_4.x86_64 libdb-utils-5.3.28-42.el8_4.x86_64 libfdisk-2.32.1-43.el8.x86_64 libffi-3.1-24.el8.x86_64 libgcc-8.5.0-20.el8.x86_64 libgcrypt-1.8.5-7.el8_6.x86_64 libgomp-8.5.0-20.el8.x86_64 libgpg-error-1.31-1.el8.x86_64 libidn2-2.2.0-1.el8.x86_64 libipt-1.6.1-8.el8.x86_64 libksba-1.3.5-9.el8_7.x86_64 libmount-2.32.1-43.el8.x86_64 libmpc-1.1.0-9.1.el8.x86_64 libnghttp2-1.33.0-5.el8_9.x86_64 libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 libpkgconf-1.4.2-1.el8.x86_64 libpsl-0.20.2-6.el8.x86_64 libpwquality-1.4.4-6.el8.x86_64 libselinux-2.9-8.el8.x86_64 libsemanage-2.9-9.el8_6.x86_64 libsepol-2.9-3.el8.x86_64 libsigsegv-2.11-5.el8.x86_64 libsmartcols-2.32.1-43.el8.x86_64 libssh-0.9.6-13.el8_9.x86_64 libssh-config-0.9.6-13.el8_9.noarch libstdc++-8.5.0-20.el8.x86_64 libstdc++-devel-8.5.0-20.el8.x86_64 libtasn1-4.13-4.el8_7.x86_64 libtirpc-1.1.4-8.el8.x86_64 libtool-ltdl-2.4.6-25.el8.x86_64 libunistring-0.9.9-3.el8.x86_64 libusbx-1.0.23-4.el8.x86_64 libutempter-1.1.6-14.el8.x86_64 libuuid-2.32.1-43.el8.x86_64 libverto-0.3.2-2.el8.x86_64 libxcrypt-4.1.1-6.el8.x86_64 libxcrypt-devel-4.1.1-6.el8.x86_64 libxml2-2.9.7-18.el8_9.x86_64 libzstd-1.4.4-1.el8.x86_64 lua-libs-5.3.4-12.el8.x86_64 lua-srpm-macros-1-3.el8.noarch lz4-libs-1.8.3-3.el8_4.x86_64 make-4.2.1-11.el8.x86_64 mpfr-3.1.6-1.el8.x86_64 ncurses-6.1-10.20180224.el8.x86_64 ncurses-base-6.1-10.20180224.el8.noarch ncurses-libs-6.1-10.20180224.el8.x86_64 nettle-3.4.1-7.el8.x86_64 npth-1.5-4.el8.x86_64 ocaml-srpm-macros-5-4.el8.noarch openblas-srpm-macros-2-2.el8.noarch openldap-2.4.46-18.el8.x86_64 openssl-libs-1.1.1k-12.el8_9.x86_64 p11-kit-0.23.22-1.el8.x86_64 p11-kit-trust-0.23.22-1.el8.x86_64 pam-1.3.1-27.el8.x86_64 patch-2.7.6-11.el8.x86_64 pcre-8.42-6.el8.x86_64 pcre2-10.32-3.el8_6.x86_64 perl-srpm-macros-1-25.el8.noarch pkgconf-1.4.2-1.el8.x86_64 pkgconf-m4-1.4.2-1.el8.noarch pkgconf-pkg-config-1.4.2-1.el8.x86_64 platform-python-3.6.8-56.el8_9.3.x86_64 platform-python-setuptools-39.2.0-7.el8.noarch popt-1.18-1.el8.x86_64 publicsuffix-list-dafsa-20180723-1.el8.noarch python-rpm-macros-3-45.el8.noarch python-srpm-macros-3-45.el8.noarch python3-libs-3.6.8-56.el8_9.3.x86_64 python3-pip-wheel-9.0.3-23.el8.noarch python3-rpm-macros-3-45.el8.noarch python3-setuptools-wheel-39.2.0-7.el8.noarch qt5-srpm-macros-5.15.3-1.el8.noarch readline-7.0-10.el8.x86_64 redhat-release-8.9-0.1.el8.x86_64 redhat-rpm-config-131-1.el8.noarch rpm-4.14.3-28.el8_9.x86_64 rpm-build-4.14.3-28.el8_9.x86_64 rpm-build-libs-4.14.3-28.el8_9.x86_64 rpm-libs-4.14.3-28.el8_9.x86_64 rust-srpm-macros-5-2.el8.noarch sed-4.5-5.el8.x86_64 setup-2.12.2-9.el8.noarch shadow-utils-4.6-19.el8.x86_64 sqlite-libs-3.26.0-19.el8_9.x86_64 systemd-libs-239-78.el8.x86_64 tar-1.30-9.el8.x86_64 tpm2-tss-2.3.2-5.el8.x86_64 tzdata-2024a-1.el8.noarch unzip-6.0-46.el8.x86_64 util-linux-2.32.1-43.el8.x86_64 which-2.21-20.el8.x86_64 xz-5.2.4-4.el8_6.x86_64 xz-libs-5.2.4-4.el8_6.x86_64 zip-3.0-23.el8.x86_64 zlib-1.2.11-25.el8.x86_64 zstd-1.4.4-1.el8.x86_64 Start: buildsrpm Start: rpmbuild -bs sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/python-pysam-0.22.0-1.el8.src.rpm Finish: rpmbuild -bs cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/rhel+epel-8-x86_64-1708464790.174803/root/var/log’: No such file or directory INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-8-x86_64-1708464790.174803/root/var/log/dnf.log /var/lib/mock/rhel+epel-8-x86_64-1708464790.174803/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-8-x86_64-1708464790.174803/root/var/log/dnf.rpm.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-wwvwxr5d/python-pysam/python-pysam.spec) Config(child) 2 minutes 3 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/python-pysam-0.22.0-1.el8.src.rpm) Config(rhel+epel-8-x86_64) Start: chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-8-x86_64-1708464790.174803/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management from host and used with --installroot: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.18.2-1.fc39.noarch python3-dnf-plugins-core-4.4.4-1.fc39.noarch yum-4.18.2-1.fc39.noarch dnf5-5.1.12-1.fc39.x86_64 dnf5-plugins-5.1.12-1.fc39.x86_64 Finish: chroot init Start: build phase for python-pysam-0.22.0-1.el8.src.rpm Start: build setup for python-pysam-0.22.0-1.el8.src.rpm sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/python-pysam-0.22.0-1.el8.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 43 kB/s | 2.2 kB 00:00 Additional repo https_copr_be_cloud_fedoraproje 63 kB/s | 2.2 kB 00:00 Red Hat Enterprise Linux - BaseOS 15 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux - AppStream 28 kB/s | 4.5 kB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 19 kB/s | 4.5 kB 00:00 Extra Packages for Enterprise Linux 8 - x86_64 1.2 MB/s | 28 kB 00:00 Package platform-python-setuptools-39.2.0-7.el8.noarch is already installed. Dependencies resolved. ============================================================================================================ Package Arch Version Repository Size ============================================================================================================ Installing: bzip2-devel x86_64 1.0.6-26.el8 rhel-baseos 224 k libcurl-devel x86_64 7.61.1-33.el8 rhel-baseos 835 k python3-sphinx noarch 1:1.7.6-3.el8 codeready-builder 1.7 M python36-devel x86_64 3.6.8-38.module+el8.9.0+20976+d3c38525 rhel-appstream 17 k xz-devel x86_64 5.2.4-4.el8_6 rhel-baseos 63 k zlib-devel x86_64 1.2.11-25.el8 rhel-baseos 59 k Installing dependencies: Lmod x86_64 8.7.32-1.el8 epel 267 k fontawesome-fonts noarch 4.7.0-5.el8_9 rhel-appstream 203 k fontawesome-fonts-web noarch 4.7.0-5.el8_9 rhel-appstream 429 k fontpackages-filesystem noarch 1.44-22.el8 rhel-baseos 16 k google-roboto-slab-fonts noarch 1.100263-0.7.20150923git.el8 codeready-builder 238 k lato-fonts noarch 2.015-5.el8 rhel-appstream 3.3 M lua x86_64 5.3.4-12.el8 rhel-appstream 192 k lua-filesystem x86_64 1.6.3-7.el8 codeready-builder 36 k lua-json noarch 1.3.2-9.el8 rhel-appstream 29 k lua-lpeg x86_64 1.0.1-6.el8 rhel-appstream 67 k lua-posix x86_64 33.3.1-9.el8 codeready-builder 176 k lua-term x86_64 0.07-9.el8 epel 16 k platform-python-devel x86_64 3.6.8-56.el8_9.3 rhel-appstream 241 k platform-python-pip noarch 9.0.3-23.el8 rhel-baseos 1.6 M procps-ng x86_64 3.3.15-14.el8 rhel-baseos 330 k python-sphinx-locale noarch 1:1.7.6-3.el8 codeready-builder 171 k python3-babel noarch 2.5.1-7.el8 rhel-appstream 4.8 M python3-chardet noarch 3.0.4-7.el8 rhel-baseos 195 k python3-docutils noarch 0.14-12.module+el8.9.0+20976+d3c38525 rhel-appstream 1.6 M python3-idna noarch 2.5-5.el8 rhel-baseos 97 k python3-imagesize noarch 1.0.0-2.el8 codeready-builder 16 k python3-jinja2 noarch 2.11.2-6.el8 copr_base 246 k python3-markupsafe x86_64 0.23-19.el8 rhel-appstream 39 k python3-mock noarch 2.0.0-11.el8 codeready-builder 59 k python3-packaging noarch 20.4-1.el8 copr_base 68 k python3-pip noarch 9.0.3-23.el8 rhel-appstream 20 k python3-pygments noarch 2.2.0-22.module+el8.9.0+20976+d3c38525 rhel-appstream 1.9 M python3-pyparsing noarch 2.1.10-7.el8 rhel-baseos 142 k python3-pysocks noarch 1.6.8-3.el8 rhel-baseos 34 k python3-pytz noarch 2017.2-11.el8 rhel-appstream 54 k python3-requests noarch 2.20.0-3.el8_8 rhel-baseos 124 k python3-rpm-generators noarch 5-8.el8 rhel-appstream 25 k python3-setuptools noarch 39.2.0-7.el8 rhel-baseos 163 k python3-six noarch 1.11.0-8.el8 rhel-baseos 38 k python3-snowballstemmer noarch 1.2.1-6.el8 codeready-builder 108 k python3-sphinx-theme-alabaster noarch 0.7.9-7.el8 codeready-builder 24 k python3-sphinx_rtd_theme noarch 0.3.1-3.el8 codeready-builder 128 k python3-sphinxcontrib-websupport noarch 1.0.1-10.20180316git.el8 codeready-builder 50 k python3-sqlalchemy x86_64 1.3.2-2.module+el8.9.0+20976+d3c38525.1 rhel-appstream 1.9 M python3-urllib3 noarch 1.24.2-5.el8_9.2 rhel-baseos 177 k python3-whoosh noarch 2.7.4-9.el8 codeready-builder 1.1 M python36 x86_64 3.6.8-38.module+el8.9.0+20976+d3c38525 rhel-appstream 19 k python36-rpm-macros noarch 3.6.8-38.module+el8.9.0+20976+d3c38525 rhel-appstream 16 k tcl x86_64 1:8.6.8-2.el8 rhel-baseos 1.1 M Enabling module streams: python36 3.6 Transaction Summary ============================================================================================================ Install 50 Packages Total download size: 24 M Installed size: 95 M Downloading Packages: (1/50): python3-packaging-20.4-1.el8.noarch.rpm 1.4 MB/s | 68 kB 00:00 (2/50): python3-jinja2-2.11.2-6.el8.noarch.rpm 3.3 MB/s | 246 kB 00:00 (3/50): fontpackages-filesystem-1.44-22.el8.noa 69 kB/s | 16 kB 00:00 (4/50): bzip2-devel-1.0.6-26.el8.x86_64.rpm 720 kB/s | 224 kB 00:00 (5/50): tcl-8.6.8-2.el8.x86_64.rpm 3.7 MB/s | 1.1 MB 00:00 (6/50): python3-idna-2.5-5.el8.noarch.rpm 661 kB/s | 97 kB 00:00 (7/50): python3-pyparsing-2.1.10-7.el8.noarch.r 1.0 MB/s | 142 kB 00:00 (8/50): python3-chardet-3.0.4-7.el8.noarch.rpm 1.0 MB/s | 195 kB 00:00 (9/50): python3-pysocks-1.6.8-3.el8.noarch.rpm 395 kB/s | 34 kB 00:00 (10/50): python3-six-1.11.0-8.el8.noarch.rpm 189 kB/s | 38 kB 00:00 (11/50): python3-setuptools-39.2.0-7.el8.noarch 1.0 MB/s | 163 kB 00:00 (12/50): xz-devel-5.2.4-4.el8_6.x86_64.rpm 213 kB/s | 63 kB 00:00 (13/50): python3-requests-2.20.0-3.el8_8.noarch 815 kB/s | 124 kB 00:00 (14/50): libcurl-devel-7.61.1-33.el8.x86_64.rpm 3.0 MB/s | 835 kB 00:00 (15/50): platform-python-pip-9.0.3-23.el8.noarc 5.3 MB/s | 1.6 MB 00:00 (16/50): zlib-devel-1.2.11-25.el8.x86_64.rpm 525 kB/s | 59 kB 00:00 (17/50): procps-ng-3.3.15-14.el8.x86_64.rpm 2.0 MB/s | 330 kB 00:00 (18/50): python3-urllib3-1.24.2-5.el8_9.2.noarc 1.3 MB/s | 177 kB 00:00 (19/50): lua-lpeg-1.0.1-6.el8.x86_64.rpm 603 kB/s | 67 kB 00:00 (20/50): lua-json-1.3.2-9.el8.noarch.rpm 125 kB/s | 29 kB 00:00 (21/50): python3-markupsafe-0.23-19.el8.x86_64. 235 kB/s | 39 kB 00:00 (22/50): lua-5.3.4-12.el8.x86_64.rpm 2.1 MB/s | 192 kB 00:00 (23/50): python3-rpm-generators-5-8.el8.noarch. 260 kB/s | 25 kB 00:00 (24/50): lato-fonts-2.015-5.el8.noarch.rpm 5.9 MB/s | 3.3 MB 00:00 (25/50): python3-babel-2.5.1-7.el8.noarch.rpm 22 MB/s | 4.8 MB 00:00 (26/50): python3-pip-9.0.3-23.el8.noarch.rpm 231 kB/s | 20 kB 00:00 (27/50): fontawesome-fonts-4.7.0-5.el8_9.noarch 2.6 MB/s | 203 kB 00:00 (28/50): python3-pytz-2017.2-11.el8.noarch.rpm 459 kB/s | 54 kB 00:00 (29/50): fontawesome-fonts-web-4.7.0-5.el8_9.no 3.6 MB/s | 429 kB 00:00 (30/50): platform-python-devel-3.6.8-56.el8_9.3 1.7 MB/s | 241 kB 00:00 (31/50): python3-pygments-2.2.0-22.module+el8.9 11 MB/s | 1.9 MB 00:00 (32/50): python3-docutils-0.14-12.module+el8.9. 7.1 MB/s | 1.6 MB 00:00 (33/50): python3-sqlalchemy-1.3.2-2.module+el8. 10 MB/s | 1.9 MB 00:00 (34/50): python36-devel-3.6.8-38.module+el8.9.0 149 kB/s | 17 kB 00:00 (35/50): python36-3.6.8-38.module+el8.9.0+20976 105 kB/s | 19 kB 00:00 (36/50): python36-rpm-macros-3.6.8-38.module+el 181 kB/s | 16 kB 00:00 (37/50): lua-filesystem-1.6.3-7.el8.x86_64.rpm 361 kB/s | 36 kB 00:00 (38/50): lua-posix-33.3.1-9.el8.x86_64.rpm 1.5 MB/s | 176 kB 00:00 (39/50): google-roboto-slab-fonts-1.100263-0.7. 1.8 MB/s | 238 kB 00:00 (40/50): python3-imagesize-1.0.0-2.el8.noarch.r 145 kB/s | 16 kB 00:00 (41/50): python3-mock-2.0.0-11.el8.noarch.rpm 488 kB/s | 59 kB 00:00 (42/50): python3-snowballstemmer-1.2.1-6.el8.no 1.2 MB/s | 108 kB 00:00 (43/50): python3-sphinx-theme-alabaster-0.7.9-7 295 kB/s | 24 kB 00:00 (44/50): python3-sphinx_rtd_theme-0.3.1-3.el8.n 1.8 MB/s | 128 kB 00:00 (45/50): python3-sphinxcontrib-websupport-1.0.1 609 kB/s | 50 kB 00:00 (46/50): python-sphinx-locale-1.7.6-3.el8.noarc 2.3 MB/s | 171 kB 00:00 (47/50): python3-whoosh-2.7.4-9.el8.noarch.rpm 8.7 MB/s | 1.1 MB 00:00 (48/50): python3-sphinx-1.7.6-3.el8.noarch.rpm 13 MB/s | 1.7 MB 00:00 (49/50): lua-term-0.07-9.el8.x86_64.rpm 212 kB/s | 16 kB 00:00 (50/50): Lmod-8.7.32-1.el8.x86_64.rpm 2.6 MB/s | 267 kB 00:00 -------------------------------------------------------------------------------- Total 9.3 MB/s | 24 MB 00:02 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-six-1.11.0-8.el8.noarch 1/50 Installing : lua-5.3.4-12.el8.x86_64 2/50 Installing : python3-setuptools-39.2.0-7.el8.noarch 3/50 Installing : fontpackages-filesystem-1.44-22.el8.noarch 4/50 Installing : fontawesome-fonts-4.7.0-5.el8_9.noarch 5/50 Installing : fontawesome-fonts-web-4.7.0-5.el8_9.noarch 6/50 Installing : lato-fonts-2.015-5.el8.noarch 7/50 Installing : lua-filesystem-1.6.3-7.el8.x86_64 8/50 Installing : python3-mock-2.0.0-11.el8.noarch 9/50 Installing : lua-term-0.07-9.el8.x86_64 10/50 Installing : python-sphinx-locale-1:1.7.6-3.el8.noarch 11/50 Installing : python3-whoosh-2.7.4-9.el8.noarch 12/50 Installing : python3-sphinx-theme-alabaster-0.7.9-7.el8.noarch 13/50 Installing : python3-snowballstemmer-1.2.1-6.el8.noarch 14/50 Installing : python3-imagesize-1.0.0-2.el8.noarch 15/50 Installing : google-roboto-slab-fonts-1.100263-0.7.20150923git. 16/50 Installing : python3-sphinx_rtd_theme-0.3.1-3.el8.noarch 17/50 Installing : lua-posix-33.3.1-9.el8.x86_64 18/50 Installing : python3-sqlalchemy-1.3.2-2.module+el8.9.0+20976+d3 19/50 Installing : python3-pytz-2017.2-11.el8.noarch 20/50 Installing : python3-babel-2.5.1-7.el8.noarch 21/50 Installing : python3-rpm-generators-5-8.el8.noarch 22/50 Installing : platform-python-devel-3.6.8-56.el8_9.3.x86_64 23/50 Installing : python3-markupsafe-0.23-19.el8.x86_64 24/50 Installing : python3-jinja2-2.11.2-6.el8.noarch 25/50 Installing : lua-lpeg-1.0.1-6.el8.x86_64 26/50 Installing : lua-json-1.3.2-9.el8.noarch 27/50 Installing : procps-ng-3.3.15-14.el8.x86_64 28/50 Installing : platform-python-pip-9.0.3-23.el8.noarch 29/50 Installing : python3-pip-9.0.3-23.el8.noarch 30/50 Installing : python36-3.6.8-38.module+el8.9.0+20976+d3c38525.x8 31/50 Running scriptlet: python36-3.6.8-38.module+el8.9.0+20976+d3c38525.x8 31/50 Installing : python3-docutils-0.14-12.module+el8.9.0+20976+d3c3 32/50 Installing : python3-pygments-2.2.0-22.module+el8.9.0+20976+d3c 33/50 Installing : python3-pysocks-1.6.8-3.el8.noarch 34/50 Installing : python3-urllib3-1.24.2-5.el8_9.2.noarch 35/50 Installing : python3-pyparsing-2.1.10-7.el8.noarch 36/50 Installing : python3-packaging-20.4-1.el8.noarch 37/50 Installing : python3-idna-2.5-5.el8.noarch 38/50 Installing : python3-chardet-3.0.4-7.el8.noarch 39/50 Installing : python3-requests-2.20.0-3.el8_8.noarch 40/50 Installing : tcl-1:8.6.8-2.el8.x86_64 41/50 Running scriptlet: tcl-1:8.6.8-2.el8.x86_64 41/50 Installing : Lmod-8.7.32-1.el8.x86_64 42/50 Running scriptlet: Lmod-8.7.32-1.el8.x86_64 42/50 Installing : python3-sphinxcontrib-websupport-1.0.1-10.20180316 43/50 Installing : python3-sphinx-1:1.7.6-3.el8.noarch 44/50 Installing : python36-devel-3.6.8-38.module+el8.9.0+20976+d3c38 45/50 Running scriptlet: python36-devel-3.6.8-38.module+el8.9.0+20976+d3c38 45/50 Installing : python36-rpm-macros-3.6.8-38.module+el8.9.0+20976+ 46/50 Installing : zlib-devel-1.2.11-25.el8.x86_64 47/50 Installing : libcurl-devel-7.61.1-33.el8.x86_64 48/50 Installing : xz-devel-5.2.4-4.el8_6.x86_64 49/50 Installing : bzip2-devel-1.0.6-26.el8.x86_64 50/50 Running scriptlet: bzip2-devel-1.0.6-26.el8.x86_64 50/50 Verifying : python3-jinja2-2.11.2-6.el8.noarch 1/50 Verifying : python3-packaging-20.4-1.el8.noarch 2/50 Verifying : bzip2-devel-1.0.6-26.el8.x86_64 3/50 Verifying : tcl-1:8.6.8-2.el8.x86_64 4/50 Verifying : fontpackages-filesystem-1.44-22.el8.noarch 5/50 Verifying : python3-chardet-3.0.4-7.el8.noarch 6/50 Verifying : python3-idna-2.5-5.el8.noarch 7/50 Verifying : python3-pyparsing-2.1.10-7.el8.noarch 8/50 Verifying : python3-pysocks-1.6.8-3.el8.noarch 9/50 Verifying : python3-six-1.11.0-8.el8.noarch 10/50 Verifying : xz-devel-5.2.4-4.el8_6.x86_64 11/50 Verifying : python3-setuptools-39.2.0-7.el8.noarch 12/50 Verifying : libcurl-devel-7.61.1-33.el8.x86_64 13/50 Verifying : platform-python-pip-9.0.3-23.el8.noarch 14/50 Verifying : python3-requests-2.20.0-3.el8_8.noarch 15/50 Verifying : zlib-devel-1.2.11-25.el8.x86_64 16/50 Verifying : procps-ng-3.3.15-14.el8.x86_64 17/50 Verifying : python3-urllib3-1.24.2-5.el8_9.2.noarch 18/50 Verifying : lato-fonts-2.015-5.el8.noarch 19/50 Verifying : lua-json-1.3.2-9.el8.noarch 20/50 Verifying : lua-lpeg-1.0.1-6.el8.x86_64 21/50 Verifying : python3-markupsafe-0.23-19.el8.x86_64 22/50 Verifying : lua-5.3.4-12.el8.x86_64 23/50 Verifying : python3-babel-2.5.1-7.el8.noarch 24/50 Verifying : python3-rpm-generators-5-8.el8.noarch 25/50 Verifying : python3-pip-9.0.3-23.el8.noarch 26/50 Verifying : python3-pytz-2017.2-11.el8.noarch 27/50 Verifying : fontawesome-fonts-4.7.0-5.el8_9.noarch 28/50 Verifying : fontawesome-fonts-web-4.7.0-5.el8_9.noarch 29/50 Verifying : platform-python-devel-3.6.8-56.el8_9.3.x86_64 30/50 Verifying : python3-docutils-0.14-12.module+el8.9.0+20976+d3c3 31/50 Verifying : python3-pygments-2.2.0-22.module+el8.9.0+20976+d3c 32/50 Verifying : python3-sqlalchemy-1.3.2-2.module+el8.9.0+20976+d3 33/50 Verifying : python36-3.6.8-38.module+el8.9.0+20976+d3c38525.x8 34/50 Verifying : python36-devel-3.6.8-38.module+el8.9.0+20976+d3c38 35/50 Verifying : python36-rpm-macros-3.6.8-38.module+el8.9.0+20976+ 36/50 Verifying : lua-filesystem-1.6.3-7.el8.x86_64 37/50 Verifying : lua-posix-33.3.1-9.el8.x86_64 38/50 Verifying : google-roboto-slab-fonts-1.100263-0.7.20150923git. 39/50 Verifying : python3-imagesize-1.0.0-2.el8.noarch 40/50 Verifying : python3-mock-2.0.0-11.el8.noarch 41/50 Verifying : python3-snowballstemmer-1.2.1-6.el8.noarch 42/50 Verifying : python3-sphinx-theme-alabaster-0.7.9-7.el8.noarch 43/50 Verifying : python3-sphinx_rtd_theme-0.3.1-3.el8.noarch 44/50 Verifying : python3-sphinxcontrib-websupport-1.0.1-10.20180316 45/50 Verifying : python3-whoosh-2.7.4-9.el8.noarch 46/50 Verifying : python-sphinx-locale-1:1.7.6-3.el8.noarch 47/50 Verifying : python3-sphinx-1:1.7.6-3.el8.noarch 48/50 Verifying : Lmod-8.7.32-1.el8.x86_64 49/50 Verifying : lua-term-0.07-9.el8.x86_64 50/50 Installed products updated. Installed: Lmod-8.7.32-1.el8.x86_64 bzip2-devel-1.0.6-26.el8.x86_64 fontawesome-fonts-4.7.0-5.el8_9.noarch fontawesome-fonts-web-4.7.0-5.el8_9.noarch fontpackages-filesystem-1.44-22.el8.noarch google-roboto-slab-fonts-1.100263-0.7.20150923git.el8.noarch lato-fonts-2.015-5.el8.noarch libcurl-devel-7.61.1-33.el8.x86_64 lua-5.3.4-12.el8.x86_64 lua-filesystem-1.6.3-7.el8.x86_64 lua-json-1.3.2-9.el8.noarch lua-lpeg-1.0.1-6.el8.x86_64 lua-posix-33.3.1-9.el8.x86_64 lua-term-0.07-9.el8.x86_64 platform-python-devel-3.6.8-56.el8_9.3.x86_64 platform-python-pip-9.0.3-23.el8.noarch procps-ng-3.3.15-14.el8.x86_64 python-sphinx-locale-1:1.7.6-3.el8.noarch python3-babel-2.5.1-7.el8.noarch python3-chardet-3.0.4-7.el8.noarch python3-docutils-0.14-12.module+el8.9.0+20976+d3c38525.noarch python3-idna-2.5-5.el8.noarch python3-imagesize-1.0.0-2.el8.noarch python3-jinja2-2.11.2-6.el8.noarch python3-markupsafe-0.23-19.el8.x86_64 python3-mock-2.0.0-11.el8.noarch python3-packaging-20.4-1.el8.noarch python3-pip-9.0.3-23.el8.noarch python3-pygments-2.2.0-22.module+el8.9.0+20976+d3c38525.noarch python3-pyparsing-2.1.10-7.el8.noarch python3-pysocks-1.6.8-3.el8.noarch python3-pytz-2017.2-11.el8.noarch python3-requests-2.20.0-3.el8_8.noarch python3-rpm-generators-5-8.el8.noarch python3-setuptools-39.2.0-7.el8.noarch python3-six-1.11.0-8.el8.noarch python3-snowballstemmer-1.2.1-6.el8.noarch python3-sphinx-1:1.7.6-3.el8.noarch python3-sphinx-theme-alabaster-0.7.9-7.el8.noarch python3-sphinx_rtd_theme-0.3.1-3.el8.noarch python3-sphinxcontrib-websupport-1.0.1-10.20180316git.el8.noarch python3-sqlalchemy-1.3.2-2.module+el8.9.0+20976+d3c38525.1.x86_64 python3-urllib3-1.24.2-5.el8_9.2.noarch python3-whoosh-2.7.4-9.el8.noarch python36-3.6.8-38.module+el8.9.0+20976+d3c38525.x86_64 python36-devel-3.6.8-38.module+el8.9.0+20976+d3c38525.x86_64 python36-rpm-macros-3.6.8-38.module+el8.9.0+20976+d3c38525.noarch tcl-1:8.6.8-2.el8.x86_64 xz-devel-5.2.4-4.el8_6.x86_64 zlib-devel-1.2.11-25.el8.x86_64 Complete! Finish: build setup for python-pysam-0.22.0-1.el8.src.rpm Start: rpmbuild python-pysam-0.22.0-1.el8.src.rpm Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.kD1KqM + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pysam-0.22.0 + /usr/bin/gzip -dc /builddir/build/SOURCES/pysam-0.22.0.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd pysam-0.22.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + rm -rf pysam.egg-info + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.vY7drI + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + /usr/bin/python3.6 setup.py build '--executable=/usr/bin/python3.6 -s' # pysam: no cython available - using pre-compiled C # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (sysconfig) CC=gcc -pthread # pysam: (env) CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld checking for gcc... gcc -pthread 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 -pthread accepts -g... yes checking for gcc -pthread 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... unknown checking how to run the C preprocessor... gcc -pthread -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... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... no checking for library containing regcomp... configure: WARNING: S3 support not enabled: requires SSL development files 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: --enable-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 hfile_libcurl.o hfile_gcs.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm -lcurl # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=1 # 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=1 # 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_64-3.6 creating build/lib.linux-x86_64-3.6/pysam copying pysam/Pileup.py -> build/lib.linux-x86_64-3.6/pysam copying pysam/__init__.py -> build/lib.linux-x86_64-3.6/pysam copying pysam/bcftools.py -> build/lib.linux-x86_64-3.6/pysam copying pysam/samtools.py -> build/lib.linux-x86_64-3.6/pysam copying pysam/utils.py -> build/lib.linux-x86_64-3.6/pysam copying pysam/version.py -> build/lib.linux-x86_64-3.6/pysam copying pysam/config.py -> build/lib.linux-x86_64-3.6/pysam creating build/lib.linux-x86_64-3.6/pysam/include copying pysam/include/__init__.py -> build/lib.linux-x86_64-3.6/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'htslib/__init__.py' not found (or not a regular file) package init file 'htslib/htslib/__init__.py' not found (or not a regular file) copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-3.6/pysam copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-3.6/pysam copying pysam/libctabix.pxd -> build/lib.linux-x86_64-3.6/pysam copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcutils.pxd -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-3.6/pysam copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-3.6/pysam copying pysam/csamtools_util.h -> build/lib.linux-x86_64-3.6/pysam copying pysam/htslib_util.h -> build/lib.linux-x86_64-3.6/pysam copying pysam/pysam_stream.h -> build/lib.linux-x86_64-3.6/pysam copying pysam/pysam_util.h -> build/lib.linux-x86_64-3.6/pysam copying pysam/version.h -> build/lib.linux-x86_64-3.6/pysam copying pysam/py.typed -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcalignedsegment.pyi -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcalignmentfile.pyi -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcbcf.pyi -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcbcftools.pyi -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcbgzf.pyi -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcfaidx.pyi -> build/lib.linux-x86_64-3.6/pysam copying pysam/libchtslib.pyi -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcsamfile.pyi -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcsamtools.pyi -> build/lib.linux-x86_64-3.6/pysam copying pysam/libctabix.pyi -> build/lib.linux-x86_64-3.6/pysam copying pysam/libctabixproxies.pyi -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcutils.pyi -> build/lib.linux-x86_64-3.6/pysam copying pysam/libcvcf.pyi -> build/lib.linux-x86_64-3.6/pysam copying pysam/version.pyi -> build/lib.linux-x86_64-3.6/pysam creating build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/bam.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/bedidx.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/sample.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/samtools.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/splaysort.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools copying samtools/config.h -> build/lib.linux-x86_64-3.6/pysam/include/samtools creating build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/bin.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/call.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/cols.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/convert.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/dist.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/filter.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/gff.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/hex.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/mw.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/read_consensus.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools copying bcftools/config.h -> build/lib.linux-x86_64-3.6/pysam/include/bcftools creating build/lib.linux-x86_64-3.6/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib copying htslib/header.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib copying htslib/hts_time_funcs.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib copying htslib/sam_internal.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib copying htslib/config.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib creating build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts_expr.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/kroundup.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib running build_ext gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kfunc.o kfunc.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o kstring.o kstring.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o bgzf.o bgzf.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o errmod.o errmod.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o faidx.o faidx.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o header.o header.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.18"' > version.h gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts.o hts.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_expr.o hts_expr.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hts_os.o hts_os.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o md5.o md5.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o multipart.o multipart.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o probaln.o probaln.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o realn.o realn.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o regidx.o regidx.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o region.o region.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o sam.o sam.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o sam_mods.o sam_mods.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf_sweep.o vcf_sweep.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o tbx.o tbx.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o textutils.o textutils.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o thread_pool.o thread_pool.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf.o vcf.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcfutils.o vcfutils.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_decode.o cram/cram_decode.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_encode.o cram/cram_encode.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_external.o cram/cram_external.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_index.o cram/cram_index.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_io.o cram/cram_io.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_stats.o cram/cram_stats.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/mFILE.o cram/mFILE.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/string_alloc.o cram/string_alloc.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -mavx2 -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -mavx512f -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -msse4.1 -mpopcnt -mssse3 -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile_libcurl.o hfile_libcurl.c gcc -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o hfile_gcs.o hfile_gcs.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 hfile_libcurl.o hfile_gcs.o ranlib libhts.a building 'pysam.libchtslib' extension creating build/temp.linux-x86_64-3.6 creating build/temp.linux-x86_64-3.6/pysam gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.6/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/htslib_util.c -o build/temp.linux-x86_64-3.6/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-3.6/pysam/libchtslib.o build/temp.linux-x86_64-3.6/pysam/htslib_util.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 htslib/hfile_libcurl.o htslib/hfile_gcs.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-3.6/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lcurl -lpython3.6m -o build/lib.linux-x86_64-3.6/pysam/libchtslib.cpython-36m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamtools' extension creating build/temp.linux-x86_64-3.6/samtools creating build/temp.linux-x86_64-3.6/samtools/lz4 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/libcsamtools.c -o build/temp.linux-x86_64-3.6/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/amplicon_stats.c.pysam.c:39: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/amplicon_stats.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam2depth.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam2depth.c.pysam.c:37: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam2depth.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_addrprg.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_addrprg.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_ampliconclip.c.pysam.c:30: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_ampliconclip.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_aux.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_aux.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_aux.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_cat.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_cat.c.pysam.c:39: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_cat.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_color.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_color.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_color.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_consensus.c.pysam.c:128: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_consensus.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_fastq.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_fastq.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_flags.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_flags.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_flags.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_import.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_import.c.pysam.c:36: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_import.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_index.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_index.c.pysam.c:29: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_index.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_lpileup.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_lpileup.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_markdup.c.pysam.c:32: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_markdup.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_mate.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_mate.c.pysam.c:29: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_mate.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_md.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_md.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_md.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_plbuf.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_plbuf.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_plcmd.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_plcmd.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_quickcheck.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_quickcheck.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_reheader.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_reheader.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_rmdup.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_rmdup.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_rmdupse.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_rmdupse.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_samples.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_samples.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_samples.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_sort.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_sort.c.pysam.c:29: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_sort.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_split.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_split.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_split.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bam_stat.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bam_stat.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bam_stat.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bamshuf.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bamshuf.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bamshuf.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bamtk.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bamtk.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bamtk.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bedcov.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bedcov.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bedcov.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/bedidx.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/bedidx.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/bedidx.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/consensus_pileup.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/consensus_pileup.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/coverage.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/coverage.c.pysam.c:36: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/coverage.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/cram_size.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/cram_size.c.pysam.c:30: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/cram_size.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/cut_target.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/cut_target.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/cut_target.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/dict.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/dict.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/dict.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/faidx.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/faidx.c.pysam.c:34: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/faidx.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/padding.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/padding.c.pysam.c:29: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/padding.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/phase.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/phase.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/phase.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/reference.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/reference.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/reference.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/reset.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/reset.c.pysam.c:30: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/reset.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/sam_opts.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/sam_opts.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/sam_opts.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/sam_utils.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/sam_utils.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/sam_utils.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/sam_view.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/sam_view.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/sam_view.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/sample.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/sample.c.pysam.c:28: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/sample.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/samtools.pysam.c -o build/temp.linux-x86_64-3.6/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/stats.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/stats.c.pysam.c:42: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/stats.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/stats_isize.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/stats_isize.c.pysam.c:27: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/stats_isize.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/tmp_file.c.pysam.c -o build/temp.linux-x86_64-3.6/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from samtools/tmp_file.c.pysam.c:30: /builddir/build/BUILD/pysam-0.22.0/htslib/config.h:158: warning: "_XOPEN_SOURCE" redefined #define _XOPEN_SOURCE 600 In file included from /usr/include/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from samtools/samtools.pysam.h:4, from samtools/tmp_file.c.pysam.c:1: /usr/include/features.h:202: note: this is the location of the previous definition # define _XOPEN_SOURCE 700 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c samtools/lz4/lz4.c -o build/temp.linux-x86_64-3.6/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-3.6/pysam/libcsamtools.o build/temp.linux-x86_64-3.6/samtools/amplicon_stats.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_consensus.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_fastq.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_import.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_samples.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-3.6/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-3.6/samtools/consensus_pileup.c.pysam.o build/temp.linux-x86_64-3.6/samtools/coverage.c.pysam.o build/temp.linux-x86_64-3.6/samtools/cram_size.c.pysam.o build/temp.linux-x86_64-3.6/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-3.6/samtools/dict.c.pysam.o build/temp.linux-x86_64-3.6/samtools/faidx.c.pysam.o build/temp.linux-x86_64-3.6/samtools/padding.c.pysam.o build/temp.linux-x86_64-3.6/samtools/phase.c.pysam.o build/temp.linux-x86_64-3.6/samtools/reference.c.pysam.o build/temp.linux-x86_64-3.6/samtools/reset.c.pysam.o build/temp.linux-x86_64-3.6/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-3.6/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-3.6/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-3.6/samtools/sample.c.pysam.o build/temp.linux-x86_64-3.6/samtools/samtools.pysam.o build/temp.linux-x86_64-3.6/samtools/stats.c.pysam.o build/temp.linux-x86_64-3.6/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-3.6/samtools/tmp_file.c.pysam.o build/temp.linux-x86_64-3.6/samtools/lz4/lz4.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lcurl -lchtslib.cpython-36m-x86_64-linux-gnu -lpython3.6m -o build/lib.linux-x86_64-3.6/pysam/libcsamtools.cpython-36m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-x86_64-3.6/bcftools gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/libcbcftools.c -o build/temp.linux-x86_64-3.6/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/HMM.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/abuf.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/bcftools.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/bin.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/ccall.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/cols.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/consensus.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/convert.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/csq.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/dist.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/em.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/extsort.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/filter.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/gff.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/gff.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/gvcf.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/hclust.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/kmin.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/main.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/mcall.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/mpileup.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/ploidy.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/prob1.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/read_consensus.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/regidx.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/reheader.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/str_finder.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/tabix.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-x86_64-3.6/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=] 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:541:14: note: in a call to allocation function ‘calloc’ declared here extern void *calloc (size_t __nmemb, size_t __size) ^~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcfview.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/vcmp.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c bcftools/version.c.pysam.c -o build/temp.linux-x86_64-3.6/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-3.6/pysam/libcbcftools.o build/temp.linux-x86_64-3.6/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/abuf.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/bcftools.pysam.o build/temp.linux-x86_64-3.6/bcftools/bin.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/cols.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/convert.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/csq.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/dist.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/em.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/extsort.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/filter.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/gff.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/gvcf.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/hclust.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/kmin.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/main.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/mcall.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/mpileup.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/ploidy.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/prob1.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/read_consensus.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/regidx.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/reheader.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/smpl_ilist.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/str_finder.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/tabix.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/tsv2vcf.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfannotate.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfbuf.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfcall.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfcnv.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfconcat.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfconvert.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcffilter.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfhead.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfindex.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfisec.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfmerge.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfnorm.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfplugin.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfquery.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfroh.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfsom.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfsort.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfstats.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcfview.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/vcmp.c.pysam.o build/temp.linux-x86_64-3.6/bcftools/version.c.pysam.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lcurl -lchtslib.cpython-36m-x86_64-linux-gnu -lpython3.6m -o build/lib.linux-x86_64-3.6/pysam/libcbcftools.cpython-36m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcutils' extension gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/libcutils.c -o build/temp.linux-x86_64-3.6/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/pysam_util.c -o build/temp.linux-x86_64-3.6/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-3.6/pysam/libcutils.o build/temp.linux-x86_64-3.6/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_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lcurl -lchtslib.cpython-36m-x86_64-linux-gnu -lcsamtools.cpython-36m-x86_64-linux-gnu -lcbcftools.cpython-36m-x86_64-linux-gnu -lpython3.6m -o build/lib.linux-x86_64-3.6/pysam/libcutils.cpython-36m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/libcalignmentfile.c -o build/temp.linux-x86_64-3.6/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:20422:20: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] (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:37143:16: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result] (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-3.6/pysam/libcalignmentfile.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lcurl -lchtslib.cpython-36m-x86_64-linux-gnu -lcutils.cpython-36m-x86_64-linux-gnu -lpython3.6m -o build/lib.linux-x86_64-3.6/pysam/libcalignmentfile.cpython-36m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/libcsamfile.c -o build/temp.linux-x86_64-3.6/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-3.6/pysam/libcsamfile.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lcurl -lchtslib.cpython-36m-x86_64-linux-gnu -lcutils.cpython-36m-x86_64-linux-gnu -lpython3.6m -o build/lib.linux-x86_64-3.6/pysam/libcsamfile.cpython-36m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/libcalignedsegment.c -o build/temp.linux-x86_64-3.6/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-3.6/pysam/libcalignedsegment.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lcurl -lchtslib.cpython-36m-x86_64-linux-gnu -lcutils.cpython-36m-x86_64-linux-gnu -lpython3.6m -o build/lib.linux-x86_64-3.6/pysam/libcalignedsegment.cpython-36m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/libctabix.c -o build/temp.linux-x86_64-3.6/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-3.6/pysam/libctabix.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lcurl -lchtslib.cpython-36m-x86_64-linux-gnu -lcutils.cpython-36m-x86_64-linux-gnu -lpython3.6m -o build/lib.linux-x86_64-3.6/pysam/libctabix.cpython-36m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/libcfaidx.c -o build/temp.linux-x86_64-3.6/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-3.6/pysam/libcfaidx.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lcurl -lchtslib.cpython-36m-x86_64-linux-gnu -lcutils.cpython-36m-x86_64-linux-gnu -lpython3.6m -o build/lib.linux-x86_64-3.6/pysam/libcfaidx.cpython-36m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/libcbcf.c -o build/temp.linux-x86_64-3.6/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:86742:18: warning: ignoring return value of ‘bcf_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] (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:81406:18: warning: ignoring return value of ‘bcf_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] (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:44506:11: warning: ignoring return value of ‘bcf_hrec_add_key’, declared with attribute warn_unused_result [-Wunused-result] bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:44532:11: warning: ignoring return value of ‘bcf_hrec_set_val’, declared with attribute warn_unused_result [-Wunused-result] 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:81090:18: warning: ignoring return value of ‘bcf_hdr_write’, declared with attribute warn_unused_result [-Wunused-result] (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-3.6/pysam/libcbcf.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lcurl -lchtslib.cpython-36m-x86_64-linux-gnu -lcutils.cpython-36m-x86_64-linux-gnu -lpython3.6m -o build/lib.linux-x86_64-3.6/pysam/libcbcf.cpython-36m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/libcbgzf.c -o build/temp.linux-x86_64-3.6/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-3.6/pysam/libcbgzf.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lcurl -lchtslib.cpython-36m-x86_64-linux-gnu -lcutils.cpython-36m-x86_64-linux-gnu -lpython3.6m -o build/lib.linux-x86_64-3.6/pysam/libcbgzf.cpython-36m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/libctabixproxies.c -o build/temp.linux-x86_64-3.6/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-3.6/pysam/libctabixproxies.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lcurl -lchtslib.cpython-36m-x86_64-linux-gnu -lcutils.cpython-36m-x86_64-linux-gnu -lpython3.6m -o build/lib.linux-x86_64-3.6/pysam/libctabixproxies.cpython-36m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -fPIC -I/builddir/build/BUILD/pysam-0.22.0/pysam -I/builddir/build/BUILD/pysam-0.22.0/htslib -I/builddir/build/BUILD/pysam-0.22.0/samtools -I/builddir/build/BUILD/pysam-0.22.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.22.0/bcftools -I/builddir/build/BUILD/pysam-0.22.0 -I/usr/include/python3.6m -c pysam/libcvcf.c -o build/temp.linux-x86_64-3.6/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.95’: pysam/libcvcf.c:29558:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] __pyx_t_11 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 873, __pyx_L1_error) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC build/temp.linux-x86_64-3.6/pysam/libcvcf.o -L/builddir/build/BUILD/pysam-0.22.0/pysam -L/builddir/build/BUILD/pysam-0.22.0 -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -Lbuild/lib.linux-x86_64-3.6/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lcurl -lchtslib.cpython-36m-x86_64-linux-gnu -lcutils.cpython-36m-x86_64-linux-gnu -lpython3.6m -o build/lib.linux-x86_64-3.6/pysam/libcvcf.cpython-36m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN + sleep 1 + PYTHONPATH=/builddir/build/BUILD/pysam-0.22.0 + sphinx-build-3 doc html Running Sphinx v1.7.6 making output directory... loading pickled environment... not yet created [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/3.6/objects.inv... WARNING: failed to reach any of the inventories with the following issues: building [mo]: targets for 0 po files that are out of date building [html]: targets for 9 source files that are out of date WARNING: intersphinx inventory 'https://docs.python.org/3.6/objects.inv' not fetchable due to : ('intersphinx inventory %r not fetchable due to %s: %s', 'https://docs.python.org/3.6/objects.inv', , ConnectionError(...)) updating environment: 9 added, 0 changed, 0 removed reading sources... [ 11%] api reading sources... [ 22%] benchmarking reading sources... [ 33%] developer reading sources... [ 44%] faq reading sources... [ 55%] glossary reading sources... [ 66%] index reading sources... [ 77%] installation reading sources... [ 88%] release reading sources... [100%] usage looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 11%] api writing output... [ 22%] benchmarking writing output... [ 33%] developer writing output... [ 44%] faq writing output... [ 55%] glossary writing output... [ 66%] index writing output... [ 77%] installation writing output... [ 88%] release writing output... [100%] usage generating indices... genindex writing additional pages... search copying static files... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 2 warnings. The HTML pages are in html. + rm -rf html/.doctrees html/.buildinfo + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Aq0pTM + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64 ++ dirname /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64 + cd pysam-0.22.0 + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + /usr/bin/python3.6 setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64 # pysam: no cython available - using pre-compiled C # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (sysconfig) CC=gcc -pthread # pysam: (env) CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld checking for gcc... gcc -pthread 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 -pthread accepts -g... yes checking for gcc -pthread 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... unknown checking how to run the C preprocessor... gcc -pthread -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... yes checking for curl_easy_pause in -lcurl... yes checking for CCHmac... no checking for library containing HMAC... no checking for library containing regcomp... configure: WARNING: S3 support not enabled: requires SSL development files 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: --enable-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 hfile_libcurl.o hfile_gcs.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm -lcurl # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=1 # 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=1 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running install running install_lib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64 creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6 creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/Pileup.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/bcftools.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/samtools.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/utils.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/version.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/config.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include copying build/lib.linux-x86_64-3.6/pysam/include/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/bam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/bam_ampliconclip.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/bam_lpileup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/bam_plbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/bedidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/consensus_pileup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/sam_opts.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/sam_utils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/sample.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/samtools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/splaysort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/stats_isize.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/tmp_file.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.6/pysam/include/samtools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/samtools creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/HMM.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/abuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/bam2bcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/bam_sample.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/bcftools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/bcftools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/bin.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/call.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/cigar_state.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/cols.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/convert.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/dbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/dist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/extsort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/filter.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/gff.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/gvcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/hclust.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/hex.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/khash_str2str.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/kheap.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/kmin.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/mw.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/ploidy.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/prob1.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/rbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/read_consensus.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/smpl_ilist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/str_finder.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/tsv2vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/utlist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/variantkey.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/vcfbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/vcmp.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.6/pysam/include/bcftools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/bcftools creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/bcf_sr_sort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/header.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/hfile_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/hts_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/hts_time_funcs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/sam_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/textutils_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/thread_pool_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/bgzf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/faidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/hfile.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/hts.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/hts_defs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/hts_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/hts_expr.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/hts_log.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/hts_os.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/kbitset.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/kfunc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/khash.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/khash_str2int.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/klist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/knetfile.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/kroundup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/kseq.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/ksort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/kstring.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/sam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/synced_bcf_reader.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/tbx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/thread_pool.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/vcf_sweep.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/include/htslib/htslib/vcfutils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.6/pysam/libcalignedsegment.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcalignmentfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcbcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcbcftools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcfaidx.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libchtslib.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcsamfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcsamtools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libctabix.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libctabixproxies.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcutils.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcvcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/cbcftools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/csamtools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/htslib_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/pysam_stream.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/pysam_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/version.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/py.typed -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcalignedsegment.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcalignmentfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcbcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcbcftools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcbgzf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcfaidx.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libchtslib.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcsamfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcsamtools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libctabix.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libctabixproxies.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcutils.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcvcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/version.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libchtslib.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcsamtools.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcbcftools.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcutils.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcalignmentfile.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcsamfile.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcalignedsegment.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libctabix.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcfaidx.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcbcf.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcbgzf.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libctabixproxies.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam copying build/lib.linux-x86_64-3.6/pysam/libcvcf.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-3.6/pysam/__pycache__/__init__.cpython-36.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-3.6/pysam/__pycache__/utils.cpython-36.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-3.6/pysam/__pycache__/Pileup.cpython-36.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-3.6/pysam/__pycache__/samtools.cpython-36.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-3.6/pysam/__pycache__/config.cpython-36.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-3.6/pysam/__pycache__/version.cpython-36.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/__pycache__ byte-compiling /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/bcftools.py to bcftools.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/include/__init__.py to __init__.cpython-36.pyc writing byte-compilation script '/tmp/tmpoz85nfxd.py' /usr/bin/python3.6 /tmp/tmpoz85nfxd.py removing /tmp/tmpoz85nfxd.py running install_egg_info 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' package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'htslib/__init__.py' not found (or not a regular file) package init file 'htslib/htslib/__init__.py' not found (or not a regular file) reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam-0.22.0-py3.6.egg-info running install_scripts + /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 0.22.0-1.el8 --unique-debug-suffix -0.22.0-1.el8.x86_64 --unique-debug-src-base python-pysam-0.22.0-1.el8.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/pysam-0.22.0 extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/libcalignedsegment.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/libcalignmentfile.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/libcbcf.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/libcbcftools.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/libcbgzf.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/libcfaidx.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/libchtslib.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/libcsamfile.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/libcsamtools.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/libctabix.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/libctabixproxies.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/libcutils.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6/site-packages/pysam/libcvcf.cpython-36m-x86_64-linux-gnu.so /usr/lib/rpm/sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match. 53824 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile '' 1 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib64/python3.6 using /usr/libexec/platform-python Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/lib/debug/usr/lib64/python3.6 using /usr/libexec/platform-python + /usr/lib/rpm/brp-python-hardlink + PYTHON3=/usr/bin/python3.6 + /usr/lib/rpm/redhat/brp-mangle-shebangs Processing files: python3-pysam-0.22.0-1.el8.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.Wvmdlr + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/doc/python3-pysam + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/doc/python3-pysam + cp -pr README.rst /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/doc/python3-pysam + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.g1wGYp + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + LICENSEDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/licenses/python3-pysam + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/licenses/python3-pysam + cp -pr bcftools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/licenses/python3-pysam + cp -pr htslib/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/licenses/python3-pysam + cp -pr samtools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/licenses/python3-pysam + cp -pr samtools/lz4/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/licenses/python3-pysam + exit 0 warning: File listed twice: /usr/share/licenses/python3-pysam/LICENSE warning: File listed twice: /usr/share/licenses/python3-pysam/LICENSE warning: File listed twice: /usr/share/licenses/python3-pysam/LICENSE Provides: libcalignedsegment.cpython-36m-x86_64-linux-gnu.so()(64bit) libcalignmentfile.cpython-36m-x86_64-linux-gnu.so()(64bit) libcbcf.cpython-36m-x86_64-linux-gnu.so()(64bit) libcbcftools.cpython-36m-x86_64-linux-gnu.so()(64bit) libcbgzf.cpython-36m-x86_64-linux-gnu.so()(64bit) libcfaidx.cpython-36m-x86_64-linux-gnu.so()(64bit) libchtslib.cpython-36m-x86_64-linux-gnu.so()(64bit) libcsamfile.cpython-36m-x86_64-linux-gnu.so()(64bit) libcsamtools.cpython-36m-x86_64-linux-gnu.so()(64bit) libctabix.cpython-36m-x86_64-linux-gnu.so()(64bit) libctabixproxies.cpython-36m-x86_64-linux-gnu.so()(64bit) libcutils.cpython-36m-x86_64-linux-gnu.so()(64bit) libcvcf.cpython-36m-x86_64-linux-gnu.so()(64bit) python3-pysam = 0.22.0-1.el8 python3-pysam(x86-64) = 0.22.0-1.el8 python3.6dist(pysam) = 0.22.0 python3dist(pysam) = 0.22.0 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_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libcbcftools.cpython-36m-x86_64-linux-gnu.so()(64bit) libchtslib.cpython-36m-x86_64-linux-gnu.so()(64bit) libcsamtools.cpython-36m-x86_64-linux-gnu.so()(64bit) libcurl.so.4()(64bit) libcutils.cpython-36m-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) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libpthread.so.0(GLIBC_2.3.2)(64bit) libpython3.6m.so.1.0()(64bit) libz.so.1()(64bit) python(abi) = 3.6 rtld(GNU_HASH) Processing files: python-pysam-doc-0.22.0-1.el8.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.3Rn6tL + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/doc/python-pysam-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/doc/python-pysam-doc + cp -pr html /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/doc/python-pysam-doc + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.5F0FzG + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + LICENSEDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/licenses/python-pysam-doc + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/licenses/python-pysam-doc + cp -pr bcftools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/licenses/python-pysam-doc + cp -pr htslib/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/licenses/python-pysam-doc + cp -pr samtools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/licenses/python-pysam-doc + cp -pr samtools/lz4/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64/usr/share/licenses/python-pysam-doc + exit 0 warning: File listed twice: /usr/share/licenses/python-pysam-doc/LICENSE warning: File listed twice: /usr/share/licenses/python-pysam-doc/LICENSE warning: File listed twice: /usr/share/licenses/python-pysam-doc/LICENSE Provides: python-pysam-doc = 0.22.0-1.el8 python-pysam-doc(x86-64) = 0.22.0-1.el8 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-pysam-debugsource-0.22.0-1.el8.x86_64 Provides: python-pysam-debugsource = 0.22.0-1.el8 python-pysam-debugsource(x86-64) = 0.22.0-1.el8 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-pysam-debuginfo-0.22.0-1.el8.x86_64 Provides: debuginfo(build-id) = 0a2e406b4a3af3248f460b2528a7c1507984f1b2 debuginfo(build-id) = 14b21c138fadd80d097fa01548f99e3247a4ea0f debuginfo(build-id) = 1a7bfbd0b49dbaac9cbb09c9a03511424ad95f0d debuginfo(build-id) = 5bf6393d7ad2dfe8b626f0fa56fe67717daf310f debuginfo(build-id) = 61e799c13b7711ffc97df429dd519c1e020740db debuginfo(build-id) = 63fb420db65a193dc0159d7c8bb69eb5f8ae90d5 debuginfo(build-id) = 750791ac51513079c1f42b4acd4a23a928983489 debuginfo(build-id) = 86e86aedb1b88041f4c8c7cf3ef6efd1f2ccffaa debuginfo(build-id) = 90231dc08326fd6da77936d7e813d59fd382c01a debuginfo(build-id) = d0b165ae97fa959cb43304ea6e5f1bbd8ec1b103 debuginfo(build-id) = d2973189a2eabf6acff86c7ceabeab6d3cc3ce98 debuginfo(build-id) = d455ea106f22f00f323974682953450ceb4118df debuginfo(build-id) = f4d5f60c9c1b78e81ae903f1002775fe5a36d29d python3-pysam-debuginfo = 0.22.0-1.el8 python3-pysam-debuginfo(x86-64) = 0.22.0-1.el8 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-pysam-debugsource(x86-64) = 0.22.0-1.el8 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64 Wrote: /builddir/build/RPMS/python3-pysam-0.22.0-1.el8.x86_64.rpm Wrote: /builddir/build/RPMS/python-pysam-doc-0.22.0-1.el8.x86_64.rpm Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.22.0-1.el8.x86_64.rpm Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.22.0-1.el8.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.4YcJoj + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-pysam-0.22.0-1.el8.x86_64 + exit 0 Finish: rpmbuild python-pysam-0.22.0-1.el8.src.rpm Finish: build phase for python-pysam-0.22.0-1.el8.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-8-x86_64-1708464790.174803/root/var/log/dnf.log /var/lib/mock/rhel+epel-8-x86_64-1708464790.174803/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-8-x86_64-1708464790.174803/root/var/log/dnf.rpm.log INFO: Done(/var/lib/copr-rpmbuild/results/python-pysam-0.22.0-1.el8.src.rpm) Config(child) 3 minutes 56 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "python-pysam-doc", "epoch": null, "version": "0.22.0", "release": "1.el8", "arch": "x86_64" }, { "name": "python-pysam", "epoch": null, "version": "0.22.0", "release": "1.el8", "arch": "src" }, { "name": "python3-pysam", "epoch": null, "version": "0.22.0", "release": "1.el8", "arch": "x86_64" }, { "name": "python3-pysam-debuginfo", "epoch": null, "version": "0.22.0", "release": "1.el8", "arch": "x86_64" }, { "name": "python-pysam-debugsource", "epoch": null, "version": "0.22.0", "release": "1.el8", "arch": "x86_64" } ] } RPMResults finished