Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c18a' (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/7377906-fedora-39-x86_64 --chroot fedora-39-x86_64 Version: 0.72 PID: 9273 Logging PID: 9274 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 7377906, 'buildroot_pkgs': [], 'chroot': 'fedora-39-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'b492991e1f7f9ea51e8c9f958b58eea7b8bd658d', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/R-Rhtslib', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'R-Rhtslib', 'package_version': '2.4.1-1', 'project_dirname': 'openblas-0.3.23', 'project_name': 'openblas-0.3.23', 'project_owner': 'psimovec', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/psimovec/openblas-0.3.23/fedora-39-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}, {'baseurl': 'http://kojipkgs.fedoraproject.org/repos/rawhide/latest/$basearch/', 'id': 'http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch', 'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch'}], 'sandbox': 'psimovec/openblas-0.3.23--https://src.fedoraproject.org/user/iucar', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'submitter': 'https://src.fedoraproject.org/user/iucar', 'tags': [], 'task_id': '7377906-fedora-39-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/R-Rhtslib /var/lib/copr-rpmbuild/workspace/workdir-b9lpwk4i/R-Rhtslib --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/R-Rhtslib', '/var/lib/copr-rpmbuild/workspace/workdir-b9lpwk4i/R-Rhtslib', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-b9lpwk4i/R-Rhtslib'... Running: git checkout b492991e1f7f9ea51e8c9f958b58eea7b8bd658d -- cmd: ['git', 'checkout', 'b492991e1f7f9ea51e8c9f958b58eea7b8bd658d', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-b9lpwk4i/R-Rhtslib rc: 0 stdout: stderr: Note: switching to 'b492991e1f7f9ea51e8c9f958b58eea7b8bd658d'. 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 b492991 automatic import of R-Rhtslib Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-b9lpwk4i/R-Rhtslib 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 Rhtslib_2.4.1.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o Rhtslib_2.4.1.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/psimovec/openblas-0.3.23/R-Rhtslib/Rhtslib_2.4.1.tar.gz/md5/b7d295a694e865f4f4060c94c4bca446/Rhtslib_2.4.1.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 4474k 100 4474k 0 0 12.6M 0 --:--:-- --:--:-- --:--:-- 12.6M INFO: Reading stdout from command: md5sum Rhtslib_2.4.1.tar.gz /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-b9lpwk4i/R-Rhtslib/R-Rhtslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-b9lpwk4i/R-Rhtslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1714171571.633590 -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-b9lpwk4i/R-Rhtslib/R-Rhtslib.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-b9lpwk4i/R-Rhtslib --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1714171571.633590 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-b9lpwk4i/R-Rhtslib/R-Rhtslib.spec) Config(fedora-39-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.5 INFO: Mock Version: 5.5 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1714171571.633590/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:39 INFO: Pulling image: registry.fedoraproject.org/fedora:39 INFO: Copy content of container registry.fedoraproject.org/fedora:39 to /var/lib/mock/fedora-39-x86_64-bootstrap-1714171571.633590/root INFO: Checking that registry.fedoraproject.org/fedora:39 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:39 with podman image mount INFO: image registry.fedoraproject.org/fedora:39 as /var/lib/containers/storage/overlay/3758ffa6c59cda3522484b75afc0404c581222c46e46c90cc5248df1211d583c/merged INFO: umounting image registry.fedoraproject.org/fedora:39 (/var/lib/containers/storage/overlay/3758ffa6c59cda3522484b75afc0404c581222c46e46c90cc5248df1211d583c/merged) with podman image umount INFO: Package manager dnf detected and used (fallback) INFO: Bootstrap image not marked ready Start(bootstrap): installing dnf tooling No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 28 MB/s | 18 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 23 MB/s | 75 MB 00:03 fedora 35 MB/s | 89 MB 00:02 updates 862 kB/s | 35 MB 00:41 Last metadata expiration check: 0:00:04 ago on Fri Apr 26 22:47:18 2024. Package python3-dnf-4.19.2-1.fc39.noarch is already installed. Dependencies resolved. ========================================================================================================================= Package Arch Version Repository Size ========================================================================================================================= Installing: python3-dnf-plugins-core noarch 4.6.0-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 302 k Upgrading: dnf noarch 4.19.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 491 k dnf-data noarch 4.19.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40 k python3-dnf noarch 4.19.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 553 k yum noarch 4.19.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k Installing dependencies: dbus-libs x86_64 1:1.14.10-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 156 k python3-dateutil noarch 1:2.8.2-13.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 345 k python3-dbus x86_64 1.3.2-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 145 k python3-distro noarch 1.9.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 45 k python3-six noarch 1.16.0-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k python3-systemd x86_64 235-9.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 100 k Transaction Summary ========================================================================================================================= Install 7 Packages Upgrade 4 Packages Total download size: 2.2 M Downloading Packages: (1/11): dbus-libs-1.14.10-3.fc40.x86_64.rpm 1.8 MB/s | 156 kB 00:00 (2/11): python3-dbus-1.3.2-6.fc40.x86_64.rpm 1.4 MB/s | 145 kB 00:00 (3/11): python3-distro-1.9.0-3.fc40.noarch.rpm 2.1 MB/s | 45 kB 00:00 (4/11): python3-dateutil-2.8.2-13.fc40.noarch.r 2.9 MB/s | 345 kB 00:00 (5/11): python3-six-1.16.0-14.fc40.noarch.rpm 1.8 MB/s | 41 kB 00:00 (6/11): python3-dnf-plugins-core-4.6.0-1.fc41.n 9.2 MB/s | 302 kB 00:00 (7/11): python3-systemd-235-9.fc40.x86_64.rpm 5.0 MB/s | 100 kB 00:00 (8/11): dnf-data-4.19.2-1.fc41.noarch.rpm 1.8 MB/s | 40 kB 00:00 (9/11): dnf-4.19.2-1.fc41.noarch.rpm 17 MB/s | 491 kB 00:00 (10/11): python3-dnf-4.19.2-1.fc41.noarch.rpm 16 MB/s | 553 kB 00:00 (11/11): yum-4.19.2-1.fc41.noarch.rpm 1.9 MB/s | 37 kB 00:00 -------------------------------------------------------------------------------- Total 13 MB/s | 2.2 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Upgrading : dnf-data-4.19.2-1.fc41.noarch 1/15 Upgrading : python3-dnf-4.19.2-1.fc41.noarch 2/15 Upgrading : dnf-4.19.2-1.fc41.noarch 3/15 Running scriptlet: dnf-4.19.2-1.fc41.noarch 3/15 Installing : python3-systemd-235-9.fc40.x86_64 4/15 Installing : python3-six-1.16.0-14.fc40.noarch 5/15 Installing : python3-dateutil-1:2.8.2-13.fc40.noarch 6/15 Installing : python3-distro-1.9.0-3.fc40.noarch 7/15 Installing : dbus-libs-1:1.14.10-3.fc40.x86_64 8/15 Installing : python3-dbus-1.3.2-6.fc40.x86_64 9/15 Installing : python3-dnf-plugins-core-4.6.0-1.fc41.noarch 10/15 Upgrading : yum-4.19.2-1.fc41.noarch 11/15 Cleanup : yum-4.19.2-1.fc39.noarch 12/15 Running scriptlet: dnf-4.19.2-1.fc39.noarch 13/15 Cleanup : dnf-4.19.2-1.fc39.noarch 13/15 Running scriptlet: dnf-4.19.2-1.fc39.noarch 13/15 Cleanup : python3-dnf-4.19.2-1.fc39.noarch 14/15 Cleanup : dnf-data-4.19.2-1.fc39.noarch 15/15 Running scriptlet: dnf-data-4.19.2-1.fc39.noarch 15/15 Verifying : dbus-libs-1:1.14.10-3.fc40.x86_64 1/15 Verifying : python3-dateutil-1:2.8.2-13.fc40.noarch 2/15 Verifying : python3-dbus-1.3.2-6.fc40.x86_64 3/15 Verifying : python3-distro-1.9.0-3.fc40.noarch 4/15 Verifying : python3-dnf-plugins-core-4.6.0-1.fc41.noarch 5/15 Verifying : python3-six-1.16.0-14.fc40.noarch 6/15 Verifying : python3-systemd-235-9.fc40.x86_64 7/15 Verifying : dnf-4.19.2-1.fc41.noarch 8/15 Verifying : dnf-4.19.2-1.fc39.noarch 9/15 Verifying : dnf-data-4.19.2-1.fc41.noarch 10/15 Verifying : dnf-data-4.19.2-1.fc39.noarch 11/15 Verifying : python3-dnf-4.19.2-1.fc41.noarch 12/15 Verifying : python3-dnf-4.19.2-1.fc39.noarch 13/15 Verifying : yum-4.19.2-1.fc41.noarch 14/15 Verifying : yum-4.19.2-1.fc39.noarch 15/15 Upgraded: dnf-4.19.2-1.fc41.noarch dnf-data-4.19.2-1.fc41.noarch python3-dnf-4.19.2-1.fc41.noarch yum-4.19.2-1.fc41.noarch Installed: dbus-libs-1:1.14.10-3.fc40.x86_64 python3-dateutil-1:2.8.2-13.fc40.noarch python3-dbus-1.3.2-6.fc40.x86_64 python3-distro-1.9.0-3.fc40.noarch python3-dnf-plugins-core-4.6.0-1.fc41.noarch python3-six-1.16.0-14.fc40.noarch python3-systemd-235-9.fc40.x86_64 Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1714171571.633590/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.19.2-1.fc41.noarch python3-dnf-plugins-core-4.6.0-1.fc41.noarch yum-4.19.2-1.fc41.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 25 MB/s | 18 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 46 MB/s | 75 MB 00:01 fedora 21 MB/s | 89 MB 00:04 updates 12 MB/s | 35 MB 00:02 Last metadata expiration check: 0:00:03 ago on Fri Apr 26 22:48:59 2024. Dependencies resolved. ======================================================================================================================================== Package Arch Version Repository Size ======================================================================================================================================== Installing group/module packages: bash x86_64 5.2.26-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 M bzip2 x86_64 1.0.8-18.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 52 k coreutils x86_64 9.5-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M cpio x86_64 2.15-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 285 k diffutils x86_64 3.10-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 397 k fedora-release-common noarch 41-0.9 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k findutils x86_64 1:4.9.0-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 482 k gawk x86_64 5.3.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M glibc-minimal-langpack x86_64 2.39.9000-16.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 110 k grep x86_64 3.11-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 290 k gzip x86_64 1.13-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 164 k info x86_64 7.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 182 k patch x86_64 2.7.6-24.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 131 k redhat-rpm-config noarch 288-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 75 k rpm-build x86_64 4.19.1.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 70 k sed x86_64 4.9-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 309 k shadow-utils x86_64 2:4.15.1-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.3 M tar x86_64 2:1.35-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 847 k unzip x86_64 6.0-63.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 185 k util-linux x86_64 2.40-13.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M which x86_64 2.21-41.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k xz x86_64 1:5.4.6-3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 532 k Installing dependencies: alternatives x86_64 1.26-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40 k ansible-srpm-macros noarch 1-15.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k audit-libs x86_64 4.0.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 126 k authselect x86_64 1.5.0-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 141 k authselect-libs x86_64 1.5.0-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 205 k basesystem noarch 11-20.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.2 k binutils x86_64 2.42.50-6.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.3 M binutils-gold x86_64 2.42.50-6.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 783 k bzip2-libs x86_64 1.0.8-18.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k ca-certificates noarch 2023.2.62_v7.0.401-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 862 k coreutils-common x86_64 9.5-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.1 M cracklib x86_64 2.9.11-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 82 k crypto-policies noarch 20240320-1.git58e3d95.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 65 k curl x86_64 8.7.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 306 k 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======================================================================================================================================== Install 153 Packages Total download size: 52 M Installed size: 179 M Downloading Packages: (1/153): ansible-srpm-macros-1-15.fc41.noarch.r 241 kB/s | 21 kB 00:00 (2/153): alternatives-1.26-3.fc40.x86_64.rpm 453 kB/s | 40 kB 00:00 (3/153): authselect-1.5.0-5.fc41.x86_64.rpm 5.5 MB/s | 141 kB 00:00 (4/153): audit-libs-4.0.1-1.fc41.x86_64.rpm 3.2 MB/s | 126 kB 00:00 (5/153): authselect-libs-1.5.0-5.fc41.x86_64.rp 7.9 MB/s | 205 kB 00:00 (6/153): basesystem-11-20.fc40.noarch.rpm 332 kB/s | 7.2 kB 00:00 (7/153): gdb-minimal-14.2-5.fc41.x86_64.rpm 23 MB/s | 4.3 MB 00:00 (8/153): binutils-gold-2.42.50-6.fc41.x86_64.rp 8.2 MB/s | 783 kB 00:00 (9/153): binutils-2.42.50-6.fc41.x86_64.rpm 42 MB/s | 6.3 MB 00:00 (10/153): bzip2-1.0.8-18.fc40.x86_64.rpm 2.4 MB/s | 52 kB 00:00 (11/153): bzip2-libs-1.0.8-18.fc40.x86_64.rpm 2.3 MB/s | 41 kB 00:00 (12/153): 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00:00 (71/153): libfdisk-2.40-13.fc41.x86_64.rpm 7.2 MB/s | 159 kB 00:00 (72/153): libevent-2.1.12-12.fc40.x86_64.rpm 7.7 MB/s | 257 kB 00:00 (73/153): libffi-3.4.6-1.fc41.x86_64.rpm 1.9 MB/s | 40 kB 00:00 (74/153): libgcc-14.0.1-0.15.fc41.x86_64.rpm 6.7 MB/s | 126 kB 00:00 (75/153): libidn2-2.3.7-1.fc40.x86_64.rpm 6.0 MB/s | 112 kB 00:00 (76/153): libgomp-14.0.1-0.15.fc41.x86_64.rpm 11 MB/s | 346 kB 00:00 (77/153): libmount-2.40-13.fc41.x86_64.rpm 7.5 MB/s | 155 kB 00:00 (78/153): libnghttp2-1.61.0-1.fc41.x86_64.rpm 4.2 MB/s | 76 kB 00:00 (79/153): libnsl2-2.0.1-1.fc40.x86_64.rpm 1.6 MB/s | 30 kB 00:00 (80/153): libpkgconf-2.1.0-1.fc40.x86_64.rpm 2.2 MB/s | 38 kB 00:00 (81/153): libpwquality-1.4.5-9.fc40.x86_64.rpm 6.0 MB/s | 108 kB 00:00 (82/153): libpsl-0.21.5-3.fc40.x86_64.rpm 3.2 MB/s | 64 kB 00:00 (83/153): libsemanage-3.6-3.fc40.x86_64.rpm 6.3 MB/s | 116 kB 00:00 (84/153): libselinux-3.6-4.fc40.x86_64.rpm 4.3 MB/s | 88 kB 00:00 (85/153): libsmartcols-2.40-13.fc41.x86_64.rpm 4.5 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Running transaction test Transaction test succeeded. 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gzip-1.13-1.fc40.x86_64 117/153 Installing : libarchive-3.7.2-3.fc41.x86_64 118/153 Installing : cracklib-2.9.11-5.fc40.x86_64 119/153 Installing : libpwquality-1.4.5-9.fc40.x86_64 120/153 Installing : authselect-1.5.0-5.fc41.x86_64 121/153 Installing : libnsl2-2.0.1-1.fc40.x86_64 122/153 Installing : pam-1.6.1-1.fc41.x86_64 123/153 Installing : libssh-0.10.6-6.fc41.x86_64 124/153 Installing : libevent-2.1.12-12.fc40.x86_64 125/153 Installing : openldap-2.6.7-1.fc40.x86_64 126/153 Installing : libcurl-8.7.1-1.fc41.x86_64 127/153 Installing : elfutils-libs-0.191-7.fc41.x86_64 128/153 Installing : elfutils-debuginfod-client-0.191-7.fc41.x86_64 129/153 Installing : binutils-gold-2.42.50-6.fc41.x86_64 130/153 Running scriptlet: binutils-gold-2.42.50-6.fc41.x86_64 130/153 Installing : binutils-2.42.50-6.fc41.x86_64 131/153 Running scriptlet: binutils-2.42.50-6.fc41.x86_64 131/153 Installing : gdb-minimal-14.2-5.fc41.x86_64 132/153 Installing : elfutils-0.191-7.fc41.x86_64 133/153 Installing : debugedit-5.0-14.fc40.x86_64 134/153 Installing : curl-8.7.1-1.fc41.x86_64 135/153 Installing : rpm-sequoia-1.6.0-2.fc40.x86_64 136/153 Installing : rpm-libs-4.19.1.1-1.fc40.x86_64 137/153 Running scriptlet: rpm-4.19.1.1-1.fc40.x86_64 138/153 Installing : rpm-4.19.1.1-1.fc40.x86_64 138/153 Installing : efi-srpm-macros-5-11.fc40.noarch 139/153 Installing : lua-srpm-macros-1-13.fc40.noarch 140/153 Installing : zig-srpm-macros-1-2.fc40.noarch 141/153 Installing : rpm-build-libs-4.19.1.1-1.fc40.x86_64 142/153 Installing : ansible-srpm-macros-1-15.fc41.noarch 143/153 Installing : fonts-srpm-macros-1:2.0.5-14.fc40.noarch 144/153 Installing : forge-srpm-macros-0.3.1-1.fc41.noarch 145/153 Installing : go-srpm-macros-3.6.0-1.fc41.noarch 146/153 Installing : python-srpm-macros-3.12-9.fc41.noarch 147/153 Installing : redhat-rpm-config-288-1.fc41.noarch 148/153 Installing : rpm-build-4.19.1.1-1.fc40.x86_64 149/153 Installing : pyproject-srpm-macros-1.12.0-1.fc40.noarch 150/153 Installing : util-linux-2.40-13.fc41.x86_64 151/153 Running scriptlet: util-linux-2.40-13.fc41.x86_64 151/153 Installing : which-2.21-41.fc40.x86_64 152/153 Installing : info-7.1-2.fc40.x86_64 153/153 Running scriptlet: filesystem-3.18-9.fc41.x86_64 153/153 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch 153/153 Running scriptlet: authselect-libs-1.5.0-5.fc41.x86_64 153/153 Running scriptlet: rpm-4.19.1.1-1.fc40.x86_64 153/153 Running scriptlet: info-7.1-2.fc40.x86_64 153/153 Installed: alternatives-1.26-3.fc40.x86_64 ansible-srpm-macros-1-15.fc41.noarch audit-libs-4.0.1-1.fc41.x86_64 authselect-1.5.0-5.fc41.x86_64 authselect-libs-1.5.0-5.fc41.x86_64 basesystem-11-20.fc40.noarch bash-5.2.26-3.fc40.x86_64 binutils-2.42.50-6.fc41.x86_64 binutils-gold-2.42.50-6.fc41.x86_64 bzip2-1.0.8-18.fc40.x86_64 bzip2-libs-1.0.8-18.fc40.x86_64 ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch coreutils-9.5-1.fc41.x86_64 coreutils-common-9.5-1.fc41.x86_64 cpio-2.15-1.fc40.x86_64 cracklib-2.9.11-5.fc40.x86_64 crypto-policies-20240320-1.git58e3d95.fc41.noarch curl-8.7.1-1.fc41.x86_64 cyrus-sasl-lib-2.1.28-19.fc40.x86_64 debugedit-5.0-14.fc40.x86_64 diffutils-3.10-5.fc40.x86_64 dwz-0.15-6.fc40.x86_64 ed-1.20.2-1.fc41.x86_64 efi-srpm-macros-5-11.fc40.noarch elfutils-0.191-7.fc41.x86_64 elfutils-debuginfod-client-0.191-7.fc41.x86_64 elfutils-default-yama-scope-0.191-7.fc41.noarch elfutils-libelf-0.191-7.fc41.x86_64 elfutils-libs-0.191-7.fc41.x86_64 fedora-gpg-keys-41-0.1.noarch fedora-release-41-0.9.noarch fedora-release-common-41-0.9.noarch fedora-release-identity-basic-41-0.9.noarch fedora-repos-41-0.1.noarch fedora-repos-rawhide-41-0.1.noarch file-5.45-5.fc41.x86_64 file-libs-5.45-5.fc41.x86_64 filesystem-3.18-9.fc41.x86_64 findutils-1:4.9.0-8.fc40.x86_64 fonts-srpm-macros-1:2.0.5-14.fc40.noarch forge-srpm-macros-0.3.1-1.fc41.noarch fpc-srpm-macros-1.3-12.fc40.noarch gawk-5.3.0-3.fc40.x86_64 gdb-minimal-14.2-5.fc41.x86_64 gdbm-1:1.23-6.fc40.x86_64 gdbm-libs-1:1.23-6.fc40.x86_64 ghc-srpm-macros-1.9.1-1.fc41.noarch glibc-2.39.9000-16.fc41.x86_64 glibc-common-2.39.9000-16.fc41.x86_64 glibc-gconv-extra-2.39.9000-16.fc41.x86_64 glibc-minimal-langpack-2.39.9000-16.fc41.x86_64 gmp-1:6.3.0-1.fc41.x86_64 gnat-srpm-macros-6-5.fc40.noarch go-srpm-macros-3.6.0-1.fc41.noarch grep-3.11-7.fc40.x86_64 gzip-1.13-1.fc40.x86_64 info-7.1-2.fc40.x86_64 jansson-2.13.1-9.fc40.x86_64 kernel-srpm-macros-1.0-23.fc41.noarch keyutils-libs-1.6.3-3.fc40.x86_64 krb5-libs-1.21.2-5.fc40.x86_64 libacl-2.3.2-1.fc40.x86_64 libarchive-3.7.2-3.fc41.x86_64 libattr-2.5.2-3.fc40.x86_64 libblkid-2.40-13.fc41.x86_64 libbrotli-1.1.0-3.fc40.x86_64 libcap-2.69-8.fc41.x86_64 libcap-ng-0.8.5-1.fc41.x86_64 libcom_err-1.47.0-5.fc40.x86_64 libcurl-8.7.1-1.fc41.x86_64 libeconf-0.6.2-1.fc41.x86_64 libevent-2.1.12-12.fc40.x86_64 libfdisk-2.40-13.fc41.x86_64 libffi-3.4.6-1.fc41.x86_64 libgcc-14.0.1-0.15.fc41.x86_64 libgomp-14.0.1-0.15.fc41.x86_64 libidn2-2.3.7-1.fc40.x86_64 libmount-2.40-13.fc41.x86_64 libnghttp2-1.61.0-1.fc41.x86_64 libnsl2-2.0.1-1.fc40.x86_64 libpkgconf-2.1.0-1.fc40.x86_64 libpsl-0.21.5-3.fc40.x86_64 libpwquality-1.4.5-9.fc40.x86_64 libselinux-3.6-4.fc40.x86_64 libsemanage-3.6-3.fc40.x86_64 libsepol-3.6-3.fc40.x86_64 libsmartcols-2.40-13.fc41.x86_64 libssh-0.10.6-6.fc41.x86_64 libssh-config-0.10.6-6.fc41.noarch libstdc++-14.0.1-0.15.fc41.x86_64 libtasn1-4.19.0-6.fc40.x86_64 libtirpc-1.3.4-1.rc3.fc41.x86_64 libtool-ltdl-2.4.7-10.fc40.x86_64 libunistring-1.1-7.fc41.x86_64 libutempter-1.2.1-13.fc40.x86_64 libuuid-2.40-13.fc41.x86_64 libverto-0.3.2-8.fc40.x86_64 libxcrypt-4.4.36-5.fc40.x86_64 libxml2-2.12.6-1.fc41.x86_64 libzstd-1.5.6-1.fc41.x86_64 lua-libs-5.4.6-5.fc40.x86_64 lua-srpm-macros-1-13.fc40.noarch lz4-libs-1.9.4-6.fc40.x86_64 mpfr-4.2.1-3.fc40.x86_64 ncurses-base-6.4-12.20240127.fc40.noarch ncurses-libs-6.4-12.20240127.fc40.x86_64 ocaml-srpm-macros-9-3.fc40.noarch openblas-srpm-macros-2-17.fc41.noarch openldap-2.6.7-1.fc40.x86_64 openssl-libs-1:3.2.1-6.fc41.x86_64 p11-kit-0.25.3-4.fc40.x86_64 p11-kit-trust-0.25.3-4.fc40.x86_64 package-notes-srpm-macros-0.5-11.fc40.noarch pam-1.6.1-1.fc41.x86_64 pam-libs-1.6.1-1.fc41.x86_64 patch-2.7.6-24.fc40.x86_64 pcre2-10.43-1.fc41.x86_64 pcre2-syntax-10.43-1.fc41.noarch perl-srpm-macros-1-53.fc40.noarch pkgconf-2.1.0-1.fc40.x86_64 pkgconf-m4-2.1.0-1.fc40.noarch pkgconf-pkg-config-2.1.0-1.fc40.x86_64 popt-1.19-6.fc40.x86_64 publicsuffix-list-dafsa-20240107-3.fc40.noarch pyproject-srpm-macros-1.12.0-1.fc40.noarch python-srpm-macros-3.12-9.fc41.noarch qt5-srpm-macros-5.15.13-1.fc41.noarch qt6-srpm-macros-6.7.0-1.fc41.noarch readline-8.2-8.fc40.x86_64 redhat-rpm-config-288-1.fc41.noarch rpm-4.19.1.1-1.fc40.x86_64 rpm-build-4.19.1.1-1.fc40.x86_64 rpm-build-libs-4.19.1.1-1.fc40.x86_64 rpm-libs-4.19.1.1-1.fc40.x86_64 rpm-sequoia-1.6.0-2.fc40.x86_64 rust-srpm-macros-26.2-1.fc41.noarch sed-4.9-1.fc40.x86_64 setup-2.14.5-2.fc40.noarch shadow-utils-2:4.15.1-2.fc41.x86_64 sqlite-libs-3.45.2-1.fc41.x86_64 systemd-libs-255.5-1.fc41.x86_64 tar-2:1.35-3.fc40.x86_64 unzip-6.0-63.fc40.x86_64 util-linux-2.40-13.fc41.x86_64 util-linux-core-2.40-13.fc41.x86_64 which-2.21-41.fc40.x86_64 xxhash-libs-0.8.2-2.fc40.x86_64 xz-1:5.4.6-3.fc41.x86_64 xz-libs-1:5.4.6-3.fc41.x86_64 zig-srpm-macros-1-2.fc40.noarch zip-3.0-40.fc40.x86_64 zlib-ng-compat-2.1.6-2.fc40.x86_64 zstd-1.5.6-1.fc41.x86_64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.26-3.fc40.x86_64 ansible-srpm-macros-1-15.fc41.noarch audit-libs-4.0.1-1.fc41.x86_64 authselect-1.5.0-5.fc41.x86_64 authselect-libs-1.5.0-5.fc41.x86_64 basesystem-11-20.fc40.noarch bash-5.2.26-3.fc40.x86_64 binutils-2.42.50-6.fc41.x86_64 binutils-gold-2.42.50-6.fc41.x86_64 bzip2-1.0.8-18.fc40.x86_64 bzip2-libs-1.0.8-18.fc40.x86_64 ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch coreutils-9.5-1.fc41.x86_64 coreutils-common-9.5-1.fc41.x86_64 cpio-2.15-1.fc40.x86_64 cracklib-2.9.11-5.fc40.x86_64 crypto-policies-20240320-1.git58e3d95.fc41.noarch curl-8.7.1-1.fc41.x86_64 cyrus-sasl-lib-2.1.28-19.fc40.x86_64 debugedit-5.0-14.fc40.x86_64 diffutils-3.10-5.fc40.x86_64 dwz-0.15-6.fc40.x86_64 ed-1.20.2-1.fc41.x86_64 efi-srpm-macros-5-11.fc40.noarch elfutils-0.191-7.fc41.x86_64 elfutils-debuginfod-client-0.191-7.fc41.x86_64 elfutils-default-yama-scope-0.191-7.fc41.noarch elfutils-libelf-0.191-7.fc41.x86_64 elfutils-libs-0.191-7.fc41.x86_64 fedora-gpg-keys-41-0.1.noarch fedora-release-41-0.9.noarch fedora-release-common-41-0.9.noarch fedora-release-identity-basic-41-0.9.noarch fedora-repos-41-0.1.noarch fedora-repos-rawhide-41-0.1.noarch file-5.45-5.fc41.x86_64 file-libs-5.45-5.fc41.x86_64 filesystem-3.18-9.fc41.x86_64 findutils-4.9.0-8.fc40.x86_64 fonts-srpm-macros-2.0.5-14.fc40.noarch forge-srpm-macros-0.3.1-1.fc41.noarch fpc-srpm-macros-1.3-12.fc40.noarch gawk-5.3.0-3.fc40.x86_64 gdb-minimal-14.2-5.fc41.x86_64 gdbm-1.23-6.fc40.x86_64 gdbm-libs-1.23-6.fc40.x86_64 ghc-srpm-macros-1.9.1-1.fc41.noarch glibc-2.39.9000-16.fc41.x86_64 glibc-common-2.39.9000-16.fc41.x86_64 glibc-gconv-extra-2.39.9000-16.fc41.x86_64 glibc-minimal-langpack-2.39.9000-16.fc41.x86_64 gmp-6.3.0-1.fc41.x86_64 gnat-srpm-macros-6-5.fc40.noarch go-srpm-macros-3.6.0-1.fc41.noarch grep-3.11-7.fc40.x86_64 gzip-1.13-1.fc40.x86_64 info-7.1-2.fc40.x86_64 jansson-2.13.1-9.fc40.x86_64 kernel-srpm-macros-1.0-23.fc41.noarch keyutils-libs-1.6.3-3.fc40.x86_64 krb5-libs-1.21.2-5.fc40.x86_64 libacl-2.3.2-1.fc40.x86_64 libarchive-3.7.2-3.fc41.x86_64 libattr-2.5.2-3.fc40.x86_64 libblkid-2.40-13.fc41.x86_64 libbrotli-1.1.0-3.fc40.x86_64 libcap-2.69-8.fc41.x86_64 libcap-ng-0.8.5-1.fc41.x86_64 libcom_err-1.47.0-5.fc40.x86_64 libcurl-8.7.1-1.fc41.x86_64 libeconf-0.6.2-1.fc41.x86_64 libevent-2.1.12-12.fc40.x86_64 libfdisk-2.40-13.fc41.x86_64 libffi-3.4.6-1.fc41.x86_64 libgcc-14.0.1-0.15.fc41.x86_64 libgomp-14.0.1-0.15.fc41.x86_64 libidn2-2.3.7-1.fc40.x86_64 libmount-2.40-13.fc41.x86_64 libnghttp2-1.61.0-1.fc41.x86_64 libnsl2-2.0.1-1.fc40.x86_64 libpkgconf-2.1.0-1.fc40.x86_64 libpsl-0.21.5-3.fc40.x86_64 libpwquality-1.4.5-9.fc40.x86_64 libselinux-3.6-4.fc40.x86_64 libsemanage-3.6-3.fc40.x86_64 libsepol-3.6-3.fc40.x86_64 libsmartcols-2.40-13.fc41.x86_64 libssh-0.10.6-6.fc41.x86_64 libssh-config-0.10.6-6.fc41.noarch libstdc++-14.0.1-0.15.fc41.x86_64 libtasn1-4.19.0-6.fc40.x86_64 libtirpc-1.3.4-1.rc3.fc41.x86_64 libtool-ltdl-2.4.7-10.fc40.x86_64 libunistring-1.1-7.fc41.x86_64 libutempter-1.2.1-13.fc40.x86_64 libuuid-2.40-13.fc41.x86_64 libverto-0.3.2-8.fc40.x86_64 libxcrypt-4.4.36-5.fc40.x86_64 libxml2-2.12.6-1.fc41.x86_64 libzstd-1.5.6-1.fc41.x86_64 lua-libs-5.4.6-5.fc40.x86_64 lua-srpm-macros-1-13.fc40.noarch lz4-libs-1.9.4-6.fc40.x86_64 mpfr-4.2.1-3.fc40.x86_64 ncurses-base-6.4-12.20240127.fc40.noarch ncurses-libs-6.4-12.20240127.fc40.x86_64 ocaml-srpm-macros-9-3.fc40.noarch openblas-srpm-macros-2-17.fc41.noarch openldap-2.6.7-1.fc40.x86_64 openssl-libs-3.2.1-6.fc41.x86_64 p11-kit-0.25.3-4.fc40.x86_64 p11-kit-trust-0.25.3-4.fc40.x86_64 package-notes-srpm-macros-0.5-11.fc40.noarch pam-1.6.1-1.fc41.x86_64 pam-libs-1.6.1-1.fc41.x86_64 patch-2.7.6-24.fc40.x86_64 pcre2-10.43-1.fc41.x86_64 pcre2-syntax-10.43-1.fc41.noarch perl-srpm-macros-1-53.fc40.noarch pkgconf-2.1.0-1.fc40.x86_64 pkgconf-m4-2.1.0-1.fc40.noarch pkgconf-pkg-config-2.1.0-1.fc40.x86_64 popt-1.19-6.fc40.x86_64 publicsuffix-list-dafsa-20240107-3.fc40.noarch pyproject-srpm-macros-1.12.0-1.fc40.noarch python-srpm-macros-3.12-9.fc41.noarch qt5-srpm-macros-5.15.13-1.fc41.noarch qt6-srpm-macros-6.7.0-1.fc41.noarch readline-8.2-8.fc40.x86_64 redhat-rpm-config-288-1.fc41.noarch rpm-4.19.1.1-1.fc40.x86_64 rpm-build-4.19.1.1-1.fc40.x86_64 rpm-build-libs-4.19.1.1-1.fc40.x86_64 rpm-libs-4.19.1.1-1.fc40.x86_64 rpm-sequoia-1.6.0-2.fc40.x86_64 rust-srpm-macros-26.2-1.fc41.noarch sed-4.9-1.fc40.x86_64 setup-2.14.5-2.fc40.noarch shadow-utils-4.15.1-2.fc41.x86_64 sqlite-libs-3.45.2-1.fc41.x86_64 systemd-libs-255.5-1.fc41.x86_64 tar-1.35-3.fc40.x86_64 unzip-6.0-63.fc40.x86_64 util-linux-2.40-13.fc41.x86_64 util-linux-core-2.40-13.fc41.x86_64 which-2.21-41.fc40.x86_64 xxhash-libs-0.8.2-2.fc40.x86_64 xz-5.4.6-3.fc41.x86_64 xz-libs-5.4.6-3.fc41.x86_64 zig-srpm-macros-1-2.fc40.noarch zip-3.0-40.fc40.x86_64 zlib-ng-compat-2.1.6-2.fc40.x86_64 zstd-1.5.6-1.fc41.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1714089600 Wrote: /builddir/build/SRPMS/R-Rhtslib-2.4.1-1.fc41.src.rpm Finish: rpmbuild -bs cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-39-x86_64-1714171571.633590/root/var/log’: No such file or directory INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-x86_64-1714171571.633590/root/var/log/dnf.log /var/lib/mock/fedora-39-x86_64-1714171571.633590/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-x86_64-1714171571.633590/root/var/log/dnf.rpm.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-b9lpwk4i/R-Rhtslib/R-Rhtslib.spec) Config(child) 3 minutes 15 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/R-Rhtslib-2.4.1-1.fc41.src.rpm) Config(fedora-39-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1714171571.633590/root. INFO: reusing tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1714171571.633590/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1714171571.633590/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.1.1-1.fc39.x86_64 rpm-sequoia-1.6.0-1.fc39.x86_64 python3-dnf-4.19.2-1.fc41.noarch python3-dnf-plugins-core-4.6.0-1.fc41.noarch yum-4.19.2-1.fc41.noarch Finish: chroot init Start: build phase for R-Rhtslib-2.4.1-1.fc41.src.rpm Start: build setup for R-Rhtslib-2.4.1-1.fc41.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1714089600 Wrote: /builddir/build/SRPMS/R-Rhtslib-2.4.1-1.fc41.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 28 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 64 kB/s | 3.8 kB 00:00 fedora 301 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http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 47 k xdg-utils noarch 1.2.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 79 k xml-common noarch 0.6.3-63.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 31 k xorg-x11-fonts-Type1 noarch 7.5-38.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 499 k xorg-x11-proto-devel noarch 2024.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 266 k Transaction Summary ============================================================================================================================================ Install 159 Packages Total download size: 276 M Installed size: 916 M Downloading Packages: (1/159): R-devel-4.4.0-1.fc41~bootstrap.x86_64. 169 kB/s | 11 kB 00:00 (2/159): R-core-devel-4.4.0-1.fc41~bootstrap.x8 869 kB/s | 88 kB 00:00 (3/159): R-java-4.4.0-1.fc41~bootstrap.x86_64.r 73 kB/s | 11 kB 00:00 (4/159): R-java-devel-4.4.0-1.fc41~bootstrap.x8 91 kB/s | 11 kB 00:00 (5/159): graphite2-devel-1.3.14-15.fc40.x86_64. 242 kB/s | 21 kB 00:00 (6/159): graphite2-1.3.14-15.fc40.x86_64.rpm 1.0 MB/s | 95 kB 00:00 (7/159): libRmath-devel-4.4.0-1.fc41~bootstrap. 462 kB/s | 16 kB 00:00 (8/159): libRmath-4.4.0-1.fc41~bootstrap.x86_64 3.1 MB/s | 124 kB 00:00 (9/159): R-rpm-macros-1.2.1-9.fc40.noarch.rpm 169 kB/s | 11 kB 00:00 (10/159): abattis-cantarell-vf-fonts-0.301-12.f 1.4 MB/s | 120 kB 00:00 (11/159): annobin-docs-12.52-1.fc41.noarch.rpm 4.3 MB/s | 90 kB 00:00 (12/159): alsa-lib-1.2.11-2.fc40.x86_64.rpm 6.5 MB/s | 499 kB 00:00 (13/159): annobin-plugin-gcc-12.52-1.fc41.x86_6 19 MB/s | 962 kB 00:00 (14/159): avahi-libs-0.8-26.fc40.x86_64.rpm 2.7 MB/s | 67 kB 00:00 (15/159): brotli-1.1.0-3.fc40.x86_64.rpm 950 kB/s | 20 kB 00:00 (16/159): brotli-devel-1.1.0-3.fc40.x86_64.rpm 1.6 MB/s | 34 kB 00:00 (17/159): bzip2-devel-1.0.8-18.fc40.x86_64.rpm 8.7 MB/s | 214 kB 00:00 (18/159): cairo-1.18.0-3.fc40.x86_64.rpm 24 MB/s | 709 kB 00:00 (19/159): cairo-devel-1.18.0-3.fc40.x86_64.rpm 5.9 MB/s | 176 kB 00:00 (20/159): cmake-filesystem-3.28.3-4.fc41.x86_64 826 kB/s | 18 kB 00:00 (21/159): copy-jdk-configs-4.1-5.fc40.noarch.rp 1.3 MB/s | 28 kB 00:00 (22/159): crypto-policies-scripts-20240320-1.gi 3.7 MB/s | 108 kB 00:00 (23/159): cups-libs-2.4.7-13.fc41.x86_64.rpm 7.9 MB/s | 259 kB 00:00 (24/159): dbus-libs-1.14.10-3.fc40.x86_64.rpm 4.8 MB/s | 156 kB 00:00 (25/159): default-fonts-core-sans-4.0-13.fc41.n 843 kB/s | 25 kB 00:00 (26/159): desktop-file-utils-0.26-12.fc40.x86_6 2.0 MB/s | 68 kB 00:00 (27/159): cpp-14.0.1-0.15.fc41.x86_64.rpm 57 MB/s | 12 MB 00:00 (28/159): emacs-filesystem-30.0-2.fc41.noarch.r 197 kB/s | 7.1 kB 00:00 (29/159): flexiblas-3.4.2-1.fc41.x86_64.rpm 1.3 MB/s | 25 kB 00:00 (30/159): expat-2.6.2-1.fc41.x86_64.rpm 4.8 MB/s | 113 kB 00:00 (31/159): flexiblas-devel-3.4.2-1.fc41.x86_64.r 5.2 MB/s | 112 kB 00:00 (32/159): flexiblas-netlib-3.4.2-1.fc41.x86_64. 34 MB/s | 3.2 MB 00:00 (33/159): flexiblas-netlib64-3.4.2-1.fc41.x86_6 32 MB/s | 3.0 MB 00:00 (34/159): flexiblas-openblas-openmp-3.4.2-1.fc4 733 kB/s | 18 kB 00:00 (35/159): flexiblas-openblas-openmp64-3.4.2-1.f 878 kB/s | 18 kB 00:00 (36/159): fontconfig-2.15.0-4.fc40.x86_64.rpm 11 MB/s | 256 kB 00:00 (37/159): fontconfig-devel-2.15.0-4.fc40.x86_64 5.5 MB/s | 129 kB 00:00 (38/159): fonts-filesystem-2.0.5-14.fc40.noarch 433 kB/s | 8.2 kB 00:00 (39/159): freetype-2.13.2-5.fc40.x86_64.rpm 15 MB/s | 410 kB 00:00 (40/159): freetype-devel-2.13.2-5.fc40.x86_64.r 18 MB/s | 913 kB 00:00 (41/159): fribidi-1.0.13-4.fc40.x86_64.rpm 3.4 MB/s | 91 kB 00:00 (42/159): gc-8.2.2-6.fc40.x86_64.rpm 5.1 MB/s | 110 kB 00:00 (43/159): gcc-c++-14.0.1-0.15.fc41.x86_64.rpm 23 MB/s | 14 MB 00:00 (44/159): R-core-4.4.0-1.fc41~bootstrap.x86_64. 30 MB/s | 63 MB 00:02 (45/159): gcc-plugin-annobin-14.0.1-0.15.fc41.x 479 kB/s | 48 kB 00:00 (46/159): gettext-0.22.5-2.fc41.x86_64.rpm 9.5 MB/s | 1.1 MB 00:00 (47/159): gettext-envsubst-0.22.5-2.fc41.x86_64 1.0 MB/s | 38 kB 00:00 (48/159): gettext-libs-0.22.5-2.fc41.x86_64.rpm 11 MB/s | 665 kB 00:00 (49/159): gettext-runtime-0.22.5-2.fc41.x86_64. 3.2 MB/s | 113 kB 00:00 (50/159): gcc-gfortran-14.0.1-0.15.fc41.x86_64. 17 MB/s | 13 MB 00:00 (51/159): glib2-devel-2.80.0-1.fc41.x86_64.rpm 17 MB/s | 1.4 MB 00:00 (52/159): glibc-devel-2.39.9000-16.fc41.x86_64. 3.0 MB/s | 121 kB 00:00 (53/159): glibc-headers-x86-2.39.9000-16.fc41.n 11 MB/s | 541 kB 00:00 (54/159): glib2-2.80.0-1.fc41.x86_64.rpm 13 MB/s | 3.0 MB 00:00 (55/159): gnutls-3.8.5-1.fc41.x86_64.rpm 17 MB/s | 1.1 MB 00:00 (56/159): google-noto-fonts-common-20240401-1.f 472 kB/s | 17 kB 00:00 (57/159): google-noto-sans-vf-fonts-20240401-1. 5.9 MB/s | 594 kB 00:00 (58/159): harfbuzz-8.4.0-1.fc41.x86_64.rpm 8.0 MB/s | 1.0 MB 00:00 (59/159): harfbuzz-devel-8.4.0-1.fc41.x86_64.rp 8.5 MB/s | 413 kB 00:00 (60/159): harfbuzz-icu-8.4.0-1.fc41.x86_64.rpm 557 kB/s | 16 kB 00:00 (61/159): gcc-14.0.1-0.15.fc41.x86_64.rpm 18 MB/s | 37 MB 00:02 (62/159): java-21-openjdk-21.0.2.0.13-3.fc41.x8 4.9 MB/s | 433 kB 00:00 (63/159): guile30-3.0.7-12.fc40.x86_64.rpm 20 MB/s | 8.0 MB 00:00 (64/159): javapackages-filesystem-6.2.0-9.fc41. 535 kB/s | 12 kB 00:00 (65/159): jbigkit-libs-2.1-29.fc40.x86_64.rpm 2.3 MB/s | 53 kB 00:00 (66/159): kernel-headers-6.9.0-0.rc5.44.fc41.x8 16 MB/s | 1.4 MB 00:00 (67/159): libICE-1.1.1-3.fc40.x86_64.rpm 3.1 MB/s | 74 kB 00:00 (68/159): libSM-1.2.4-3.fc40.x86_64.rpm 1.8 MB/s | 43 kB 00:00 (69/159): libX11-1.8.9-1.fc41.x86_64.rpm 15 MB/s | 648 kB 00:00 (70/159): libX11-common-1.8.9-1.fc41.noarch.rpm 6.3 MB/s | 145 kB 00:00 (71/159): libX11-devel-1.8.9-1.fc41.x86_64.rpm 16 MB/s | 912 kB 00:00 (72/159): libX11-xcb-1.8.9-1.fc41.x86_64.rpm 505 kB/s | 12 kB 00:00 (73/159): libXau-1.0.11-6.fc40.x86_64.rpm 1.5 MB/s | 32 kB 00:00 (74/159): libXau-devel-1.0.11-6.fc40.x86_64.rpm 699 kB/s | 14 kB 00:00 (75/159): libXcomposite-0.4.6-3.fc40.x86_64.rpm 1.2 MB/s | 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libcurl-devel-8.7.1-1.fc41.x86_64.rpm 15 MB/s | 756 kB 00:00 (91/159): libffi-devel-3.4.6-1.fc41.x86_64.rpm 989 kB/s | 29 kB 00:00 (92/159): libfontenc-1.1.8-1.fc41.x86_64.rpm 1.2 MB/s | 32 kB 00:00 (93/159): libgfortran-14.0.1-0.15.fc41.x86_64.r 7.7 MB/s | 932 kB 00:00 (94/159): libicu-devel-74.2-1.fc40.x86_64.rpm 9.5 MB/s | 855 kB 00:00 (95/159): libjpeg-turbo-3.0.2-2.fc41.x86_64.rpm 6.6 MB/s | 226 kB 00:00 (96/159): liblerc-4.0.0-6.fc40.x86_64.rpm 6.2 MB/s | 210 kB 00:00 (97/159): libmount-devel-2.40-13.fc41.x86_64.rp 1.1 MB/s | 27 kB 00:00 (98/159): libmpc-1.3.1-5.fc40.x86_64.rpm 3.3 MB/s | 71 kB 00:00 (99/159): libpng-1.6.40-3.fc40.x86_64.rpm 5.4 MB/s | 120 kB 00:00 (100/159): libpng-devel-1.6.40-3.fc40.x86_64.rp 7.0 MB/s | 291 kB 00:00 (101/159): libquadmath-14.0.1-0.15.fc41.x86_64. 5.7 MB/s | 195 kB 00:00 (102/159): libquadmath-devel-14.0.1-0.15.fc41.x 1.6 MB/s | 37 kB 00:00 (103/159): libselinux-devel-3.6-4.fc40.x86_64.r 4.8 MB/s | 115 kB 00:00 (104/159): 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pcre2-devel-10.43-1.fc41.x86_64.rpm 10 MB/s | 487 kB 00:00 (134/159): pcre2-utf16-10.43-1.fc41.x86_64.rpm 5.9 MB/s | 222 kB 00:00 (135/159): pcre2-utf32-10.43-1.fc41.x86_64.rpm 8.1 MB/s | 209 kB 00:00 (136/159): pixman-devel-0.43.4-1.fc41.x86_64.rp 724 kB/s | 17 kB 00:00 (137/159): pixman-0.43.4-1.fc41.x86_64.rpm 8.1 MB/s | 293 kB 00:00 (138/159): python3-3.12.3-2.fc41.x86_64.rpm 1.0 MB/s | 27 kB 00:00 (139/159): python-pip-wheel-24.0-2.fc41.noarch. 14 MB/s | 1.5 MB 00:00 (140/159): python3-packaging-24.0-1.fc41.noarch 4.6 MB/s | 116 kB 00:00 (141/159): sysprof-capture-devel-46.0-1.fc41.x8 2.1 MB/s | 54 kB 00:00 (142/159): tcl-8.6.14-1.fc41.x86_64.rpm 9.8 MB/s | 1.1 MB 00:00 (143/159): tcl-devel-8.6.14-1.fc41.x86_64.rpm 4.3 MB/s | 163 kB 00:00 (144/159): tk-8.6.14-1.fc41.x86_64.rpm 14 MB/s | 1.6 MB 00:00 (145/159): tk-devel-8.6.14-1.fc41.x86_64.rpm 6.9 MB/s | 489 kB 00:00 (146/159): tre-0.8.0-43.20140228gitc2f5d13.fc40 1.9 MB/s | 43 kB 00:00 (147/159): tre-common-0.8.0-43.20140228gitc2f5d 1.3 MB/s | 31 kB 00:00 (148/159): tre-devel-0.8.0-43.20140228gitc2f5d1 551 kB/s | 12 kB 00:00 (149/159): ttmkfdir-3.0.9-70.fc40.x86_64.rpm 2.5 MB/s | 56 kB 00:00 (150/159): tzdata-2024a-5.fc41.noarch.rpm 10 MB/s | 431 kB 00:00 (151/159): tzdata-java-2024a-5.fc41.noarch.rpm 2.2 MB/s | 47 kB 00:00 (152/159): xdg-utils-1.2.1-1.fc41.noarch.rpm 3.0 MB/s | 79 kB 00:00 (153/159): xml-common-0.6.3-63.fc40.noarch.rpm 1.5 MB/s | 31 kB 00:00 (154/159): xorg-x11-fonts-Type1-7.5-38.fc40.noa 12 MB/s | 499 kB 00:00 (155/159): xorg-x11-proto-devel-2024.1-1.fc41.n 8.4 MB/s | 266 kB 00:00 (156/159): xz-devel-5.4.6-3.fc41.x86_64.rpm 2.5 MB/s | 62 kB 00:00 (157/159): zlib-ng-compat-devel-2.1.6-2.fc40.x8 1.6 MB/s | 36 kB 00:00 (158/159): java-21-openjdk-headless-21.0.2.0.13 15 MB/s | 48 MB 00:03 (159/159): python3-libs-3.12.3-2.fc41.x86_64.rp 8.4 MB/s | 8.8 MB 00:01 -------------------------------------------------------------------------------- Total 43 MB/s | 276 MB 00:06 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: copy-jdk-configs-4.1-5.fc40.noarch 1/1 Running scriptlet: crypto-policies-scripts-20240320-1.git58e3d95.fc41.n 1/1 Running scriptlet: java-21-openjdk-headless-1:21.0.2.0.13-3.fc41.x86_64 1/1 Preparing : 1/1 Installing : zlib-ng-compat-devel-2.1.6-2.fc40.x86_64 1/159 Installing : xorg-x11-proto-devel-2024.1-1.fc41.noarch 2/159 Installing : nspr-4.35.0-22.fc41.x86_64 3/159 Installing : libgfortran-14.0.1-0.15.fc41.x86_64 4/159 Installing : nss-util-3.99.0-1.fc41.x86_64 5/159 Installing : libquadmath-14.0.1-0.15.fc41.x86_64 6/159 Installing : libpng-2:1.6.40-3.fc40.x86_64 7/159 Installing : libmpc-1.3.1-5.fc40.x86_64 8/159 Installing : tcl-1:8.6.14-1.fc41.x86_64 9/159 Installing : libicu-74.2-1.fc40.x86_64 10/159 Installing : fonts-filesystem-1:2.0.5-14.fc40.noarch 11/159 Installing : libicu-devel-74.2-1.fc40.x86_64 12/159 Installing : tcl-devel-1:8.6.14-1.fc41.x86_64 13/159 Installing : libpng-devel-2:1.6.40-3.fc40.x86_64 14/159 Installing : 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cups-libs-1:2.4.7-13.fc41.x86_64 dbus-libs-1:1.14.10-3.fc40.x86_64 default-fonts-core-sans-4.0-13.fc41.noarch desktop-file-utils-0.26-12.fc40.x86_64 emacs-filesystem-1:30.0-2.fc41.noarch expat-2.6.2-1.fc41.x86_64 flexiblas-3.4.2-1.fc41.x86_64 flexiblas-devel-3.4.2-1.fc41.x86_64 flexiblas-netlib-3.4.2-1.fc41.x86_64 flexiblas-netlib64-3.4.2-1.fc41.x86_64 flexiblas-openblas-openmp-3.4.2-1.fc41.x86_64 flexiblas-openblas-openmp64-3.4.2-1.fc41.x86_64 fontconfig-2.15.0-4.fc40.x86_64 fontconfig-devel-2.15.0-4.fc40.x86_64 fonts-filesystem-1:2.0.5-14.fc40.noarch freetype-2.13.2-5.fc40.x86_64 freetype-devel-2.13.2-5.fc40.x86_64 fribidi-1.0.13-4.fc40.x86_64 gc-8.2.2-6.fc40.x86_64 gcc-14.0.1-0.15.fc41.x86_64 gcc-c++-14.0.1-0.15.fc41.x86_64 gcc-gfortran-14.0.1-0.15.fc41.x86_64 gcc-plugin-annobin-14.0.1-0.15.fc41.x86_64 gettext-0.22.5-2.fc41.x86_64 gettext-envsubst-0.22.5-2.fc41.x86_64 gettext-libs-0.22.5-2.fc41.x86_64 gettext-runtime-0.22.5-2.fc41.x86_64 glib2-2.80.0-1.fc41.x86_64 glib2-devel-2.80.0-1.fc41.x86_64 glibc-devel-2.39.9000-16.fc41.x86_64 glibc-headers-x86-2.39.9000-16.fc41.noarch gnutls-3.8.5-1.fc41.x86_64 google-noto-fonts-common-20240401-1.fc41.noarch google-noto-sans-vf-fonts-20240401-1.fc41.noarch graphite2-1.3.14-15.fc40.x86_64 graphite2-devel-1.3.14-15.fc40.x86_64 guile30-3.0.7-12.fc40.x86_64 harfbuzz-8.4.0-1.fc41.x86_64 harfbuzz-devel-8.4.0-1.fc41.x86_64 harfbuzz-icu-8.4.0-1.fc41.x86_64 java-21-openjdk-1:21.0.2.0.13-3.fc41.x86_64 java-21-openjdk-devel-1:21.0.2.0.13-3.fc41.x86_64 java-21-openjdk-headless-1:21.0.2.0.13-3.fc41.x86_64 javapackages-filesystem-6.2.0-9.fc41.noarch jbigkit-libs-2.1-29.fc40.x86_64 kernel-headers-6.9.0-0.rc5.44.fc41.x86_64 libICE-1.1.1-3.fc40.x86_64 libRmath-4.4.0-1.fc41~bootstrap.x86_64 libRmath-devel-4.4.0-1.fc41~bootstrap.x86_64 libSM-1.2.4-3.fc40.x86_64 libX11-1.8.9-1.fc41.x86_64 libX11-common-1.8.9-1.fc41.noarch libX11-devel-1.8.9-1.fc41.x86_64 libX11-xcb-1.8.9-1.fc41.x86_64 libXau-1.0.11-6.fc40.x86_64 libXau-devel-1.0.11-6.fc40.x86_64 libXcomposite-0.4.6-3.fc40.x86_64 libXext-1.3.6-1.fc40.x86_64 libXext-devel-1.3.6-1.fc40.x86_64 libXft-2.3.8-6.fc40.x86_64 libXft-devel-2.3.8-6.fc40.x86_64 libXi-1.8.1-5.fc40.x86_64 libXmu-1.2.1-1.fc41.x86_64 libXrender-0.9.11-6.fc40.x86_64 libXrender-devel-0.9.11-6.fc40.x86_64 libXt-1.3.0-3.fc40.x86_64 libXtst-1.2.4-6.fc40.x86_64 libb2-0.98.1-11.fc40.x86_64 libblkid-devel-2.40-13.fc41.x86_64 libcurl-devel-8.7.1-1.fc41.x86_64 libdatrie-0.2.13-9.fc40.x86_64 libffi-devel-3.4.6-1.fc41.x86_64 libfontenc-1.1.8-1.fc41.x86_64 libgfortran-14.0.1-0.15.fc41.x86_64 libicu-74.2-1.fc40.x86_64 libicu-devel-74.2-1.fc40.x86_64 libjpeg-turbo-3.0.2-2.fc41.x86_64 liblerc-4.0.0-6.fc40.x86_64 libmount-devel-2.40-13.fc41.x86_64 libmpc-1.3.1-5.fc40.x86_64 libpng-2:1.6.40-3.fc40.x86_64 libpng-devel-2:1.6.40-3.fc40.x86_64 libquadmath-14.0.1-0.15.fc41.x86_64 libquadmath-devel-14.0.1-0.15.fc41.x86_64 libselinux-devel-3.6-4.fc40.x86_64 libsepol-devel-3.6-3.fc40.x86_64 libstdc++-devel-14.0.1-0.15.fc41.x86_64 libtextstyle-0.22.5-2.fc41.x86_64 libthai-0.1.29-8.fc40.x86_64 libtiff-4.6.0-2.fc40.x86_64 libtirpc-devel-1.3.4-1.rc3.fc41.x86_64 libwebp-1.4.0-1.fc41.x86_64 libxcb-1.17.0-1.fc41.x86_64 libxcb-devel-1.17.0-1.fc41.x86_64 libxcrypt-devel-4.4.36-5.fc40.x86_64 libxml2-devel-2.12.6-1.fc41.x86_64 lksctp-tools-1.0.19-6.fc40.x86_64 lua-5.4.6-5.fc40.x86_64 lua-posix-36.2.1-6.fc40.x86_64 make-1:4.4.1-6.fc40.x86_64 mkfontscale-1.2.2-6.fc40.x86_64 mpdecimal-2.5.1-9.fc40.x86_64 nettle-3.9.1-6.fc40.x86_64 nspr-4.35.0-22.fc41.x86_64 nss-3.99.0-1.fc41.x86_64 nss-softokn-3.99.0-1.fc41.x86_64 nss-softokn-freebl-3.99.0-1.fc41.x86_64 nss-sysinit-3.99.0-1.fc41.x86_64 nss-util-3.99.0-1.fc41.x86_64 openblas-0.3.26-4.fc40.x86_64 openblas-openmp-0.3.26-4.fc40.x86_64 openblas-openmp64-0.3.26-4.fc40.x86_64 pango-1.52.2-1.fc41.x86_64 pcre2-devel-10.43-1.fc41.x86_64 pcre2-utf16-10.43-1.fc41.x86_64 pcre2-utf32-10.43-1.fc41.x86_64 pixman-0.43.4-1.fc41.x86_64 pixman-devel-0.43.4-1.fc41.x86_64 python-pip-wheel-24.0-2.fc41.noarch python3-3.12.3-2.fc41.x86_64 python3-libs-3.12.3-2.fc41.x86_64 python3-packaging-24.0-1.fc41.noarch sysprof-capture-devel-46.0-1.fc41.x86_64 tcl-1:8.6.14-1.fc41.x86_64 tcl-devel-1:8.6.14-1.fc41.x86_64 tk-1:8.6.14-1.fc41.x86_64 tk-devel-1:8.6.14-1.fc41.x86_64 tre-0.8.0-43.20140228gitc2f5d13.fc40.x86_64 tre-common-0.8.0-43.20140228gitc2f5d13.fc40.noarch tre-devel-0.8.0-43.20140228gitc2f5d13.fc40.x86_64 ttmkfdir-3.0.9-70.fc40.x86_64 tzdata-2024a-5.fc41.noarch tzdata-java-2024a-5.fc41.noarch xdg-utils-1.2.1-1.fc41.noarch xml-common-0.6.3-63.fc40.noarch xorg-x11-fonts-Type1-7.5-38.fc40.noarch xorg-x11-proto-devel-2024.1-1.fc41.noarch xz-devel-1:5.4.6-3.fc41.x86_64 zlib-ng-compat-devel-2.1.6-2.fc40.x86_64 Complete! Finish: build setup for R-Rhtslib-2.4.1-1.fc41.src.rpm Start: rpmbuild R-Rhtslib-2.4.1-1.fc41.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1714089600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.u36mY1 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf Rhtslib + /usr/bin/mkdir -p Rhtslib + cd Rhtslib + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/Rhtslib_2.4.1.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + rm -rf /builddir/build/BUILD/Rhtslib-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/Rhtslib-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + pushd Rhtslib ~/build/BUILD/Rhtslib/Rhtslib ~/build/BUILD/Rhtslib Patch #0 (R-Rhtslib-zlibbioc.patch): + echo 'Patch #0 (R-Rhtslib-zlibbioc.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file DESCRIPTION patching file NAMESPACE Patch #1 (R-Rhtslib-buildroot-fix.patch): + echo 'Patch #1 (R-Rhtslib-buildroot-fix.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file src/Makevars.common + popd ~/build/BUILD/Rhtslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.SfUQ13 + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd Rhtslib + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.mEWM5j + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64 ++ dirname /builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd Rhtslib + mkdir -p /builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64/usr/lib64/R/library + R CMD INSTALL -l /builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64/usr/lib64/R/library Rhtslib * installing *source* package ‘Rhtslib’ ... ** using non-staged installation via StagedInstall field ** libs using C compiler: ‘gcc (GCC) 14.0.1 20240411 (Red Hat 14.0.1-0)’ cd "htslib-1.15.1" && make -f "Makefile.Rhtslib" make[1]: Entering directory '/builddir/build/BUILD/Rhtslib/Rhtslib/src/htslib-1.15.1' gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c echo '#define HTS_VERSION_TEXT "1.15.1"' > version.h echo '#define HTS_CC "gcc"' > config_vars.h echo '#define HTS_CPPFLAGS "-I/usr/local/include -D_FILE_OFFSET_BITS=64"' >> config_vars.h echo '#define HTS_CFLAGS "-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden"' >> config_vars.h echo '#define HTS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -fvisibility=hidden"' >> config_vars.h echo '#define HTS_LIBS "-lz -lm -lbz2 -llzma -lcurl"' >> config_vars.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c In file included from htscodecs/htscodecs/rANS_static4x16pr.c:74: In function ‘RansEncPutSymbol’, inlined from ‘rans_compress_O1_4x16.isra.0’ at htscodecs/htscodecs/rANS_static4x16pr.c:810:2: htscodecs/htscodecs/rANS_word.h:303:28: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 303 | *pptr = (uint8_t *)(ptr-c); | ~~~~^~~ htscodecs/htscodecs/rANS_static4x16pr.c: In function ‘rans_compress_O1_4x16.isra.0’: htscodecs/htscodecs/rANS_static4x16pr.c:793:14: note: ‘ptr’ was declared here 793 | uint8_t* ptr = out_end; | ^~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c hfile_libcurl.c: In function ‘libcurl_open’: hfile_libcurl.c:1335:9: warning: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’ is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD, | ^~ In file included from hfile_libcurl.c:47: /usr/include/curl/curl.h:2879:3: note: declared here 2879 | CURLINFO_CONTENT_LENGTH_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o ranlib libhts.a gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.pico kfunc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.pico kstring.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.pico bgzf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.pico errmod.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.pico faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o header.pico header.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.pico hfile.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.pico hts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.pico hts_expr.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.pico hts_os.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.pico md5.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.pico multipart.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.pico probaln.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.pico realn.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.pico regidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o region.pico region.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.pico sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.pico vcf_sweep.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.pico tbx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.pico textutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.pico thread_pool.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.pico vcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.pico vcfutils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.pico cram/cram_decode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.pico cram/cram_encode.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.pico cram/cram_external.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.pico cram/cram_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.pico cram/cram_io.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.pico cram/cram_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.pico cram/mFILE.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.pico cram/string_alloc.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/arith_dynamic.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/fqzcomp_qual.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/htscodecs.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.pico htscodecs/htscodecs/pack.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static4x16pr.c In file included from htscodecs/htscodecs/rANS_static4x16pr.c:74: In function ‘RansEncPutSymbol’, inlined from ‘rans_compress_O1_4x16.isra.0’ at htscodecs/htscodecs/rANS_static4x16pr.c:810:2: htscodecs/htscodecs/rANS_word.h:303:28: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 303 | *pptr = (uint8_t *)(ptr-c); | ~~~~^~~ htscodecs/htscodecs/rANS_static4x16pr.c: In function ‘rans_compress_O1_4x16.isra.0’: htscodecs/htscodecs/rANS_static4x16pr.c:793:14: note: ‘ptr’ was declared here 793 | uint8_t* ptr = out_end; | ^~~ gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rANS_static.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rle.pico htscodecs/htscodecs/rle.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/tokenise_name3.pico htscodecs/htscodecs/tokenise_name3.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fpic -fvisibility=hidden -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.pico hfile_libcurl.c hfile_libcurl.c: In function ‘libcurl_open’: hfile_libcurl.c:1335:9: warning: ‘CURLINFO_CONTENT_LENGTH_DOWNLOAD’ is deprecated: since 7.55.0. Use CURLINFO_CONTENT_LENGTH_DOWNLOAD_T [-Wdeprecated-declarations] 1335 | if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD, | ^~ In file included from hfile_libcurl.c:47: /usr/include/curl/curl.h:2879:3: note: declared here 2879 | CURLINFO_CONTENT_LENGTH_DOWNLOAD | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-soname,libhts.so.3 -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -fvisibility=hidden -o libhts.so kfunc.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hts.pico hts_expr.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_stats.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/string_alloc.pico htscodecs/htscodecs/arith_dynamic.pico htscodecs/htscodecs/fqzcomp_qual.pico htscodecs/htscodecs/htscodecs.pico htscodecs/htscodecs/pack.pico htscodecs/htscodecs/rANS_static4x16pr.pico htscodecs/htscodecs/rANS_static.pico htscodecs/htscodecs/rle.pico htscodecs/htscodecs/tokenise_name3.pico hfile_libcurl.pico -lz -lm -lbz2 -llzma -lcurl -lpthread ln -sf libhts.so libhts.so.3 make[1]: Leaving directory '/builddir/build/BUILD/Rhtslib/Rhtslib/src/htslib-1.15.1' mkdir -p "/builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64/usr/lib64/R/library/Rhtslib/include/htslib" cd "htslib-1.15.1/htslib" && cp * "/builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64/usr/lib64/R/library/Rhtslib/include/htslib" gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"htslib-1.15.1" -I/usr/local/include -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c R_init_Rhtslib.c -o R_init_Rhtslib.o mkdir -p "/builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64/usr/lib64/R/library/Rhtslib/usrlib" cd "htslib-1.15.1" && cp libhts.so libhts.a "/builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64/usr/lib64/R/library/Rhtslib/usrlib" cd "/builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64/usr/lib64/R/library/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2 gcc -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -o Rhtslib.so R_init_Rhtslib.o /builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64/usr/lib64/R/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/usr/lib64/R/lib -lR mkdir -p "/builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64/usr/lib64/R/library/Rhtslib/testdata/tabix" cd "htslib-1.15.1/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64/usr/lib64/R/library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64/usr/lib64/R/library/Rhtslib/testdata/tabix" 2>/dev/null || true) installing to /builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64/usr/lib64/R/library/Rhtslib/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘Rhtslib’ finding HTML links ... done Rhtslib-package html pkgconfig html ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Rhtslib) + test -d Rhtslib/src + cd Rhtslib/src + rm -f R_init_Rhtslib.o Rhtslib.so + rm -f /builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64/usr/lib64/R/library/R.css + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 2.4.1-1.fc41 --unique-debug-suffix -2.4.1-1.fc41.x86_64 --unique-debug-src-base R-Rhtslib-2.4.1-1.fc41.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/Rhtslib find-debuginfo: starting Extracting debug info from 2 files DWARF-compressing 2 files sepdebugcrcfix: Updated 2 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/R-Rhtslib-2.4.1-1.fc41.x86_64 5051 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.7Sri5j + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd Rhtslib + RPM_EC=0 ++ jobs -p + exit 0 Processing files: R-Rhtslib-2.4.1-1.fc41.x86_64 Provides: R(Rhtslib) = 2.4.1 R-Rhtslib = 2.4.1-1.fc41 R-Rhtslib(x86-64) = 2.4.1-1.fc41 libhts.so.3()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: R(ABI) = 4.4 R-core libR.so()(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libcurl.so.4()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Suggests: R(BiocStyle) R(knitr) R(rmarkdown) Processing files: R-Rhtslib-devel-2.4.1-1.fc41.x86_64 Provides: R-Rhtslib-devel = 2.4.1-1.fc41 R-Rhtslib-devel(x86-64) = 2.4.1-1.fc41 R-Rhtslib-static = 2.4.1-1.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-Rhtslib-debugsource-2.4.1-1.fc41.x86_64 Provides: R-Rhtslib-debugsource = 2.4.1-1.fc41 R-Rhtslib-debugsource(x86-64) = 2.4.1-1.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-Rhtslib-debuginfo-2.4.1-1.fc41.x86_64 Provides: R-Rhtslib-debuginfo = 2.4.1-1.fc41 R-Rhtslib-debuginfo(x86-64) = 2.4.1-1.fc41 debuginfo(build-id) = 78822c8c0b58d09cccd2b2354210ef7b293c90e3 debuginfo(build-id) = a009676204559fbebf7014f88b428f63f1dc3424 libhts.so-2.4.1-1.fc41.x86_64.debug()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-Rhtslib-debugsource(x86-64) = 2.4.1-1.fc41 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64 Wrote: /builddir/build/RPMS/R-Rhtslib-2.4.1-1.fc41.x86_64.rpm Wrote: /builddir/build/RPMS/R-Rhtslib-debuginfo-2.4.1-1.fc41.x86_64.rpm Wrote: /builddir/build/RPMS/R-Rhtslib-devel-2.4.1-1.fc41.x86_64.rpm Wrote: /builddir/build/RPMS/R-Rhtslib-debugsource-2.4.1-1.fc41.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.7qmoY5 + umask 022 + cd /builddir/build/BUILD + cd Rhtslib + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-Rhtslib-2.4.1-1.fc41.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.5w5b2W + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/Rhtslib-SPECPARTS + rm -rf Rhtslib Rhtslib.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild R-Rhtslib-2.4.1-1.fc41.src.rpm Finish: build phase for R-Rhtslib-2.4.1-1.fc41.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-x86_64-1714171571.633590/root/var/log/dnf.log /var/lib/mock/fedora-39-x86_64-1714171571.633590/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-x86_64-1714171571.633590/root/var/log/dnf.rpm.log INFO: Done(/var/lib/copr-rpmbuild/results/R-Rhtslib-2.4.1-1.fc41.src.rpm) 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 Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "R-Rhtslib", "epoch": null, "version": "2.4.1", "release": "1.fc41", "arch": "src" }, { "name": "R-Rhtslib-debugsource", "epoch": null, "version": "2.4.1", "release": "1.fc41", "arch": "x86_64" }, { "name": "R-Rhtslib-debuginfo", "epoch": null, "version": "2.4.1", "release": "1.fc41", "arch": "x86_64" }, { "name": "R-Rhtslib", "epoch": null, "version": "2.4.1", "release": "1.fc41", "arch": "x86_64" }, { "name": "R-Rhtslib-devel", "epoch": null, "version": "2.4.1", "release": "1.fc41", "arch": "x86_64" } ] } RPMResults finished