Warning: Permanently added '18.208.166.210' (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/7377988-fedora-39-aarch64 --chroot fedora-39-aarch64 Version: 0.72 PID: 6664 Logging PID: 6665 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 7377988, 'buildroot_pkgs': [], 'chroot': 'fedora-39-aarch64', 'enable_net': False, 'fedora_review': False, 'git_hash': '5a92d695c66d4bfeb1aba10282a09d224842eb22', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/R-Rsamtools', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'R-Rsamtools', 'package_version': '2.18.0-1', '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-aarch64/', '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': '7377988-fedora-39-aarch64', '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-Rsamtools /var/lib/copr-rpmbuild/workspace/workdir-h4p4rxnq/R-Rsamtools --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/R-Rsamtools', '/var/lib/copr-rpmbuild/workspace/workdir-h4p4rxnq/R-Rsamtools', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-h4p4rxnq/R-Rsamtools'... Running: git checkout 5a92d695c66d4bfeb1aba10282a09d224842eb22 -- cmd: ['git', 'checkout', '5a92d695c66d4bfeb1aba10282a09d224842eb22', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-h4p4rxnq/R-Rsamtools rc: 0 stdout: stderr: Note: switching to '5a92d695c66d4bfeb1aba10282a09d224842eb22'. 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 5a92d69 automatic import of R-Rsamtools Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-h4p4rxnq/R-Rsamtools 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 Rsamtools_2.18.0.tar.gz INFO: Reading stdout from command: curl --help all /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 2850k 100 2850k 0 0 125M 0 --:--:-- --:--:-- --:--:-- 126M INFO: Reading stdout from command: md5sum Rsamtools_2.18.0.tar.gz Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-h4p4rxnq/R-Rsamtools/R-Rsamtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-h4p4rxnq/R-Rsamtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1714176089.513502 -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-h4p4rxnq/R-Rsamtools/R-Rsamtools.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-h4p4rxnq/R-Rsamtools --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1714176089.513502 -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-h4p4rxnq/R-Rsamtools/R-Rsamtools.spec) Config(fedora-39-aarch64) 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-aarch64-bootstrap-1714176089.513502/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-aarch64-bootstrap-1714176089.513502/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/7bf71dd5387f226da846436ea2b3dcc6e725c0be4db2da88eb29060833db6acc/merged INFO: umounting image registry.fedoraproject.org/fedora:39 (/var/lib/containers/storage/overlay/7bf71dd5387f226da846436ea2b3dcc6e725c0be4db2da88eb29060833db6acc/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 109 MB/s | 17 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 5.0 MB/s | 74 MB 00:14 fedora 15 MB/s | 86 MB 00:05 updates 6.4 MB/s | 34 MB 00:05 Last metadata expiration check: 0:00:03 ago on Sat Apr 27 00:02:45 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 aarch64 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 aarch64 1.3.2-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 146 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 aarch64 235-9.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 101 k Transaction Summary ========================================================================================================================== Install 7 Packages Upgrade 4 Packages Total download size: 2.2 M Downloading Packages: (1/11): python3-dbus-1.3.2-6.fc40.aarch64.rpm 1.7 MB/s | 146 kB 00:00 (2/11): python3-distro-1.9.0-3.fc40.noarch.rpm 1.8 MB/s | 45 kB 00:00 (3/11): dbus-libs-1.14.10-3.fc40.aarch64.rpm 1.1 MB/s | 156 kB 00:00 (4/11): python3-dnf-plugins-core-4.6.0-1.fc41.n 6.8 MB/s | 302 kB 00:00 (5/11): python3-dateutil-2.8.2-13.fc40.noarch.r 2.1 MB/s | 345 kB 00:00 (6/11): python3-six-1.16.0-14.fc40.noarch.rpm 1.8 MB/s | 41 kB 00:00 (7/11): python3-systemd-235-9.fc40.aarch64.rpm 2.7 MB/s | 101 kB 00:00 (8/11): dnf-4.19.2-1.fc41.noarch.rpm 15 MB/s | 491 kB 00:00 (9/11): dnf-data-4.19.2-1.fc41.noarch.rpm 1.1 MB/s | 40 kB 00:00 (10/11): yum-4.19.2-1.fc41.noarch.rpm 1.3 MB/s | 37 kB 00:00 (11/11): python3-dnf-4.19.2-1.fc41.noarch.rpm 8.0 MB/s | 553 kB 00:00 -------------------------------------------------------------------------------- Total 8.5 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.aarch64 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.aarch64 8/15 Installing : python3-dbus-1.3.2-6.fc40.aarch64 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.aarch64 1/15 Verifying : python3-dateutil-1:2.8.2-13.fc40.noarch 2/15 Verifying : python3-dbus-1.3.2-6.fc40.aarch64 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.aarch64 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.aarch64 python3-dateutil-1:2.8.2-13.fc40.noarch python3-dbus-1.3.2-6.fc40.aarch64 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.aarch64 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-aarch64-1714176089.513502/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.aarch64 rpm-sequoia-1.6.0-1.fc39.aarch64 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 106 MB/s | 17 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 8.5 MB/s | 74 MB 00:08 fedora 50 MB/s | 86 MB 00:01 updates 34 MB/s | 34 MB 00:00 Last metadata expiration check: 0:00:03 ago on Sat Apr 27 00:03:48 2024. Dependencies resolved. ========================================================================================================================================= Package Arch Version Repository Size ========================================================================================================================================= Installing group/module packages: bash aarch64 5.2.26-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 M bzip2 aarch64 1.0.8-18.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 52 k coreutils aarch64 9.5-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M cpio aarch64 2.15-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 285 k diffutils aarch64 3.10-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 395 k fedora-release-common noarch 41-0.9 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k findutils aarch64 1:4.9.0-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 489 k gawk aarch64 5.3.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.0 M glibc-minimal-langpack aarch64 2.39.9000-16.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 110 k grep aarch64 3.11-7.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 288 k gzip aarch64 1.13-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 163 k info aarch64 7.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 183 k patch aarch64 2.7.6-24.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 130 k redhat-rpm-config noarch 288-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 75 k rpm-build aarch64 4.19.1.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 72 k sed aarch64 4.9-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 307 k shadow-utils aarch64 2:4.15.1-2.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.3 M tar aarch64 2:1.35-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 848 k unzip aarch64 6.0-63.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 185 k util-linux aarch64 2.40-13.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M which aarch64 2.21-41.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 42 k xz aarch64 1:5.4.6-3.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 533 k Installing dependencies: alternatives aarch64 1.26-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k ansible-srpm-macros noarch 1-15.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k audit-libs aarch64 4.0.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 126 k authselect aarch64 1.5.0-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 141 k authselect-libs aarch64 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 aarch64 2.42.50-6.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.8 M binutils-gold aarch64 2.42.50-6.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 968 k bzip2-libs aarch64 1.0.8-18.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 43 k ca-certificates noarch 2023.2.62_v7.0.401-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 862 k coreutils-common aarch64 9.5-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.1 M cracklib aarch64 2.9.11-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 83 k crypto-policies noarch 20240320-1.git58e3d95.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 65 k curl aarch64 8.7.1-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 306 k cyrus-sasl-lib aarch64 2.1.28-19.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 779 k debugedit aarch64 5.0-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 79 k dwz aarch64 0.15-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 137 k ed aarch64 1.20.2-1.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 81 k efi-srpm-macros noarch 5-11.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k elfutils aarch64 0.191-7.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 562 k elfutils-debuginfod-client aarch64 0.191-7.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 38 k elfutils-default-yama-scope noarch 0.191-7.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 k elfutils-libelf aarch64 0.191-7.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 209 k elfutils-libs aarch64 0.191-7.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 264 k fedora-gpg-keys noarch 41-0.1 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 121 k fedora-release noarch 41-0.9 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 11 k fedora-release-identity-basic noarch 41-0.9 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 12 k fedora-repos noarch 41-0.1 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 9.3 k fedora-repos-rawhide noarch 41-0.1 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 8.9 k file aarch64 5.45-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 50 k file-libs aarch64 5.45-5.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 763 k filesystem aarch64 3.18-9.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M fonts-srpm-macros noarch 1:2.0.5-14.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 27 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========================================================================================================================================= Install 153 Packages Total download size: 52 M Installed size: 307 M Downloading Packages: (1/153): gdb-minimal-14.2-5.fc41.aarch64.rpm 106 MB/s | 4.1 MB 00:00 (2/153): ansible-srpm-macros-1-15.fc41.noarch.r 303 kB/s | 21 kB 00:00 (3/153): alternatives-1.26-3.fc40.aarch64.rpm 376 kB/s | 39 kB 00:00 (4/153): authselect-1.5.0-5.fc41.aarch64.rpm 3.4 MB/s | 141 kB 00:00 (5/153): basesystem-11-20.fc40.noarch.rpm 331 kB/s | 7.2 kB 00:00 (6/153): audit-libs-4.0.1-1.fc41.aarch64.rpm 1.0 MB/s | 126 kB 00:00 (7/153): authselect-libs-1.5.0-5.fc41.aarch64.r 3.3 MB/s | 205 kB 00:00 (8/153): bash-5.2.26-3.fc40.aarch64.rpm 37 MB/s | 1.8 MB 00:00 (9/153): binutils-gold-2.42.50-6.fc41.aarch64.r 31 MB/s | 968 kB 00:00 (10/153): bzip2-1.0.8-18.fc40.aarch64.rpm 2.0 MB/s | 52 kB 00:00 (11/153): bzip2-libs-1.0.8-18.fc40.aarch64.rpm 2.1 MB/s | 43 kB 00:00 (12/153): ca-certificates-2023.2.62_v7.0.401-6. 30 MB/s | 862 kB 00:00 (13/153): binutils-2.42.50-6.fc41.aarch64.rpm 69 MB/s | 6.8 MB 00:00 (14/153): coreutils-common-9.5-1.fc41.aarch64.r 58 MB/s | 2.1 MB 00:00 (15/153): cpio-2.15-1.fc40.aarch64.rpm 9.9 MB/s | 285 kB 00:00 (16/153): cracklib-2.9.11-5.fc40.aarch64.rpm 3.7 MB/s | 83 kB 00:00 (17/153): coreutils-9.5-1.fc41.aarch64.rpm 13 MB/s | 1.1 MB 00:00 (18/153): curl-8.7.1-1.fc41.aarch64.rpm 14 MB/s | 306 kB 00:00 (19/153): crypto-policies-20240320-1.git58e3d95 2.5 MB/s | 65 kB 00:00 (20/153): debugedit-5.0-14.fc40.aarch64.rpm 3.0 MB/s | 79 kB 00:00 (21/153): diffutils-3.10-5.fc40.aarch64.rpm 13 MB/s | 395 kB 00:00 (22/153): cyrus-sasl-lib-2.1.28-19.fc40.aarch64 15 MB/s | 779 kB 00:00 (23/153): dwz-0.15-6.fc40.aarch64.rpm 4.8 MB/s | 137 kB 00:00 (24/153): ed-1.20.2-1.fc41.aarch64.rpm 3.9 MB/s | 81 kB 00:00 (25/153): efi-srpm-macros-5-11.fc40.noarch.rpm 820 kB/s | 22 kB 00:00 (26/153): elfutils-0.191-7.fc41.aarch64.rpm 24 MB/s | 562 kB 00:00 (27/153): elfutils-debuginfod-client-0.191-7.fc 1.4 MB/s | 38 kB 00:00 (28/153): elfutils-default-yama-scope-0.191-7.f 686 kB/s | 13 kB 00:00 (29/153): elfutils-libs-0.191-7.fc41.aarch64.rp 13 MB/s | 264 kB 00:00 (30/153): elfutils-libelf-0.191-7.fc41.aarch64. 7.7 MB/s | 209 kB 00:00 (31/153): fedora-gpg-keys-41-0.1.noarch.rpm 4.8 MB/s | 121 kB 00:00 (32/153): fedora-release-common-41-0.9.noarch.r 944 kB/s | 22 kB 00:00 (33/153): fedora-release-41-0.9.noarch.rpm 389 kB/s | 11 kB 00:00 (34/153): fedora-release-identity-basic-41-0.9. 493 kB/s | 12 kB 00:00 (35/153): fedora-repos-rawhide-41-0.1.noarch.rp 480 kB/s | 8.9 kB 00:00 (36/153): fedora-repos-41-0.1.noarch.rpm 379 kB/s | 9.3 kB 00:00 (37/153): file-5.45-5.fc41.aarch64.rpm 1.6 MB/s | 50 kB 00:00 (38/153): file-libs-5.45-5.fc41.aarch64.rpm 24 MB/s | 763 kB 00:00 (39/153): filesystem-3.18-9.fc41.aarch64.rpm 32 MB/s | 1.1 MB 00:00 (40/153): findutils-4.9.0-8.fc40.aarch64.rpm 14 MB/s | 489 kB 00:00 (41/153): forge-srpm-macros-0.3.1-1.fc41.noarch 926 kB/s | 19 kB 00:00 (42/153): fonts-srpm-macros-2.0.5-14.fc40.noarc 839 kB/s | 27 kB 00:00 (43/153): fpc-srpm-macros-1.3-12.fc40.noarch.rp 300 kB/s | 7.8 kB 00:00 (44/153): gawk-5.3.0-3.fc40.aarch64.rpm 36 MB/s | 1.0 MB 00:00 (45/153): gdbm-1.23-6.fc40.aarch64.rpm 4.3 MB/s | 149 kB 00:00 (46/153): gdbm-libs-1.23-6.fc40.aarch64.rpm 2.4 MB/s | 56 kB 00:00 (47/153): ghc-srpm-macros-1.9.1-1.fc41.noarch.r 348 kB/s | 9.0 kB 00:00 (48/153): glibc-2.39.9000-16.fc41.aarch64.rpm 69 MB/s | 1.9 MB 00:00 (49/153): glibc-common-2.39.9000-16.fc41.aarch6 14 MB/s | 387 kB 00:00 (50/153): glibc-gconv-extra-2.39.9000-16.fc41.a 58 MB/s | 2.0 MB 00:00 (51/153): glibc-minimal-langpack-2.39.9000-16.f 4.1 MB/s | 110 kB 00:00 (52/153): gmp-6.3.0-1.fc41.aarch64.rpm 8.4 MB/s | 270 kB 00:00 (53/153): go-srpm-macros-3.6.0-1.fc41.noarch.rp 1.4 MB/s | 28 kB 00:00 (54/153): gnat-srpm-macros-6-5.fc40.noarch.rpm 352 kB/s | 8.8 kB 00:00 (55/153): grep-3.11-7.fc40.aarch64.rpm 13 MB/s | 288 kB 00:00 (56/153): info-7.1-2.fc40.aarch64.rpm 9.3 MB/s | 183 kB 00:00 (57/153): gzip-1.13-1.fc40.aarch64.rpm 6.4 MB/s | 163 kB 00:00 (58/153): jansson-2.13.1-9.fc40.aarch64.rpm 2.2 MB/s | 46 kB 00:00 (59/153): keyutils-libs-1.6.3-3.fc40.aarch64.rp 1.4 MB/s | 32 kB 00:00 (60/153): kernel-srpm-macros-1.0-23.fc41.noarch 388 kB/s | 9.8 kB 00:00 (61/153): krb5-libs-1.21.2-5.fc40.aarch64.rpm 23 MB/s | 768 kB 00:00 (62/153): libarchive-3.7.2-3.fc41.aarch64.rpm 17 MB/s | 405 kB 00:00 (63/153): libacl-2.3.2-1.fc40.aarch64.rpm 1.0 MB/s | 25 kB 00:00 (64/153): libattr-2.5.2-3.fc40.aarch64.rpm 714 kB/s | 18 kB 00:00 (65/153): libbrotli-1.1.0-3.fc40.aarch64.rpm 14 MB/s | 346 kB 00:00 (66/153): libblkid-2.40-13.fc41.aarch64.rpm 4.8 MB/s | 126 kB 00:00 (67/153): libcap-ng-0.8.5-1.fc41.aarch64.rpm 1.5 MB/s | 32 kB 00:00 (68/153): libcom_err-1.47.0-5.fc40.aarch64.rpm 931 kB/s | 25 kB 00:00 (69/153): libcap-2.69-8.fc41.aarch64.rpm 2.3 MB/s | 87 kB 00:00 (70/153): libcurl-8.7.1-1.fc41.aarch64.rpm 13 MB/s | 350 kB 00:00 (71/153): libeconf-0.6.2-1.fc41.aarch64.rpm 1.6 MB/s | 32 kB 00:00 (72/153): libevent-2.1.12-12.fc40.aarch64.rpm 9.8 MB/s | 255 kB 00:00 (73/153): libfdisk-2.40-13.fc41.aarch64.rpm 6.1 MB/s | 157 kB 00:00 (74/153): libffi-3.4.6-1.fc41.aarch64.rpm 1.5 MB/s | 38 kB 00:00 (75/153): libgcc-14.0.1-0.15.fc41.aarch64.rpm 4.2 MB/s | 109 kB 00:00 (76/153): libidn2-2.3.7-1.fc40.aarch64.rpm 5.6 MB/s | 113 kB 00:00 (77/153): libgomp-14.0.1-0.15.fc41.aarch64.rpm 13 MB/s | 336 kB 00:00 (78/153): libmount-2.40-13.fc41.aarch64.rpm 5.9 MB/s | 154 kB 00:00 (79/153): libnghttp2-1.61.0-1.fc41.aarch64.rpm 2.9 MB/s | 77 kB 00:00 (80/153): libnsl2-2.0.1-1.fc40.aarch64.rpm 1.3 MB/s | 30 kB 00:00 (81/153): libpkgconf-2.1.0-1.fc40.aarch64.rpm 1.6 MB/s | 38 kB 00:00 (82/153): libpwquality-1.4.5-9.fc40.aarch64.rpm 5.2 MB/s | 109 kB 00:00 (83/153): libpsl-0.21.5-3.fc40.aarch64.rpm 2.4 MB/s | 64 kB 00:00 (84/153): libselinux-3.6-4.fc40.aarch64.rpm 4.5 MB/s | 88 kB 00:00 (85/153): libsemanage-3.6-3.fc40.aarch64.rpm 4.4 MB/s | 115 kB 00:00 (86/153): libsepol-3.6-3.fc40.aarch64.rpm 14 MB/s | 327 kB 00:00 (87/153): libsmartcols-2.40-13.fc41.aarch64.rpm 2.9 MB/s | 83 kB 00:00 (88/153): libssh-config-0.10.6-6.fc41.noarch.rp 450 kB/s | 9.1 kB 00:00 (89/153): libssh-0.10.6-6.fc41.aarch64.rpm 8.3 MB/s | 214 kB 00:00 (90/153): libstdc++-14.0.1-0.15.fc41.aarch64.rp 34 MB/s | 825 kB 00:00 (91/153): libtirpc-1.3.4-1.rc3.fc41.aarch64.rpm 4.5 MB/s | 94 kB 00:00 (92/153): libtasn1-4.19.0-6.fc40.aarch64.rpm 2.8 MB/s | 73 kB 00:00 (93/153): libtool-ltdl-2.4.7-10.fc40.aarch64.rp 1.2 MB/s | 36 kB 00:00 (94/153): libunistring-1.1-7.fc41.aarch64.rpm 25 MB/s | 544 kB 00:00 (95/153): libutempter-1.2.1-13.fc40.aarch64.rpm 1.1 MB/s | 27 kB 00:00 (96/153): libverto-0.3.2-8.fc40.aarch64.rpm 1.0 MB/s | 21 kB 00:00 (97/153): libuuid-2.40-13.fc41.aarch64.rpm 1.1 MB/s | 28 kB 00:00 (98/153): libxcrypt-4.4.36-5.fc40.aarch64.rpm 4.2 MB/s | 123 kB 00:00 (99/153): libzstd-1.5.6-1.fc41.aarch64.rpm 13 MB/s | 287 kB 00:00 (100/153): libxml2-2.12.6-1.fc41.aarch64.rpm 23 MB/s | 687 kB 00:00 (101/153): lua-libs-5.4.6-5.fc40.aarch64.rpm 6.6 MB/s | 131 kB 00:00 (102/153): lua-srpm-macros-1-13.fc40.noarch.rpm 341 kB/s | 8.7 kB 00:00 (103/153): lz4-libs-1.9.4-6.fc40.aarch64.rpm 3.2 MB/s | 68 kB 00:00 (104/153): mpfr-4.2.1-3.fc40.aarch64.rpm 11 MB/s | 324 kB 00:00 (105/153): ncurses-base-6.4-12.20240127.fc40.no 2.8 MB/s | 64 kB 00:00 (106/153): ncurses-libs-6.4-12.20240127.fc40.aa 13 MB/s | 329 kB 00:00 (107/153): ocaml-srpm-macros-9-3.fc40.noarch.rp 435 kB/s | 9.1 kB 00:00 (108/153): openldap-2.6.7-1.fc40.aarch64.rpm 12 MB/s | 252 kB 00:00 (109/153): openblas-srpm-macros-2-17.fc41.noarc 290 kB/s | 7.7 kB 00:00 (110/153): p11-kit-trust-0.25.3-4.fc40.aarch64. 7.0 MB/s | 142 kB 00:00 (111/153): openssl-libs-3.2.1-6.fc41.aarch64.rp 57 MB/s | 2.2 MB 00:00 (112/153): p11-kit-0.25.3-4.fc40.aarch64.rpm 18 MB/s | 486 kB 00:00 (113/153): package-notes-srpm-macros-0.5-11.fc4 351 kB/s | 9.9 kB 00:00 (114/153): pam-1.6.1-1.fc41.aarch64.rpm 20 MB/s | 527 kB 00:00 (115/153): pam-libs-1.6.1-1.fc41.aarch64.rpm 2.1 MB/s | 57 kB 00:00 (116/153): pcre2-10.43-1.fc41.aarch64.rpm 11 MB/s | 226 kB 00:00 (117/153): patch-2.7.6-24.fc40.aarch64.rpm 4.9 MB/s | 130 kB 00:00 (118/153): pcre2-syntax-10.43-1.fc41.noarch.rpm 5.5 MB/s | 149 kB 00:00 (119/153): pkgconf-2.1.0-1.fc40.aarch64.rpm 2.2 MB/s | 44 kB 00:00 (120/153): perl-srpm-macros-1-53.fc40.noarch.rp 307 kB/s | 8.4 kB 00:00 (121/153): pkgconf-m4-2.1.0-1.fc40.noarch.rpm 543 kB/s | 14 kB 00:00 (122/153): pkgconf-pkg-config-2.1.0-1.fc40.aarc 352 kB/s | 9.7 kB 00:00 (123/153): popt-1.19-6.fc40.aarch64.rpm 2.2 MB/s | 60 kB 00:00 (124/153): publicsuffix-list-dafsa-20240107-3.f 1.9 MB/s | 58 kB 00:00 (125/153): python-srpm-macros-3.12-9.fc41.noarc 1.1 MB/s | 24 kB 00:00 (126/153): pyproject-srpm-macros-1.12.0-1.fc40. 557 kB/s | 14 kB 00:00 (127/153): qt5-srpm-macros-5.15.13-1.fc41.noarc 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Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-9.fc41.aarch64 1/1 Preparing : 1/1 Installing : libgcc-14.0.1-0.15.fc41.aarch64 1/153 Running scriptlet: libgcc-14.0.1-0.15.fc41.aarch64 1/153 Installing : crypto-policies-20240320-1.git58e3d95.fc41.noarc 2/153 Running scriptlet: crypto-policies-20240320-1.git58e3d95.fc41.noarc 2/153 Installing : fedora-release-identity-basic-41-0.9.noarch 3/153 Installing : fedora-repos-rawhide-41-0.1.noarch 4/153 Installing : fedora-gpg-keys-41-0.1.noarch 5/153 Installing : fedora-repos-41-0.1.noarch 6/153 Installing : fedora-release-common-41-0.9.noarch 7/153 Installing : fedora-release-41-0.9.noarch 8/153 Installing : setup-2.14.5-2.fc40.noarch 9/153 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.5-2.fc40.noarch 9/153 Installing : filesystem-3.18-9.fc41.aarch64 10/153 Installing : basesystem-11-20.fc40.noarch 11/153 Installing : rust-srpm-macros-26.2-1.fc41.noarch 12/153 Installing : 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rpm-build-4.19.1.1-1.fc40.aarch64 149/153 Installing : pyproject-srpm-macros-1.12.0-1.fc40.noarch 150/153 Installing : util-linux-2.40-13.fc41.aarch64 151/153 Running scriptlet: util-linux-2.40-13.fc41.aarch64 151/153 Installing : which-2.21-41.fc40.aarch64 152/153 Installing : info-7.1-2.fc40.aarch64 153/153 Running scriptlet: filesystem-3.18-9.fc41.aarch64 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.aarch64 153/153 Running scriptlet: rpm-4.19.1.1-1.fc40.aarch64 153/153 Running scriptlet: info-7.1-2.fc40.aarch64 153/153 Installed: alternatives-1.26-3.fc40.aarch64 ansible-srpm-macros-1-15.fc41.noarch audit-libs-4.0.1-1.fc41.aarch64 authselect-1.5.0-5.fc41.aarch64 authselect-libs-1.5.0-5.fc41.aarch64 basesystem-11-20.fc40.noarch bash-5.2.26-3.fc40.aarch64 binutils-2.42.50-6.fc41.aarch64 binutils-gold-2.42.50-6.fc41.aarch64 bzip2-1.0.8-18.fc40.aarch64 bzip2-libs-1.0.8-18.fc40.aarch64 ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch coreutils-9.5-1.fc41.aarch64 coreutils-common-9.5-1.fc41.aarch64 cpio-2.15-1.fc40.aarch64 cracklib-2.9.11-5.fc40.aarch64 crypto-policies-20240320-1.git58e3d95.fc41.noarch curl-8.7.1-1.fc41.aarch64 cyrus-sasl-lib-2.1.28-19.fc40.aarch64 debugedit-5.0-14.fc40.aarch64 diffutils-3.10-5.fc40.aarch64 dwz-0.15-6.fc40.aarch64 ed-1.20.2-1.fc41.aarch64 efi-srpm-macros-5-11.fc40.noarch elfutils-0.191-7.fc41.aarch64 elfutils-debuginfod-client-0.191-7.fc41.aarch64 elfutils-default-yama-scope-0.191-7.fc41.noarch elfutils-libelf-0.191-7.fc41.aarch64 elfutils-libs-0.191-7.fc41.aarch64 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.aarch64 file-libs-5.45-5.fc41.aarch64 filesystem-3.18-9.fc41.aarch64 findutils-1:4.9.0-8.fc40.aarch64 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.aarch64 gdb-minimal-14.2-5.fc41.aarch64 gdbm-1:1.23-6.fc40.aarch64 gdbm-libs-1:1.23-6.fc40.aarch64 ghc-srpm-macros-1.9.1-1.fc41.noarch glibc-2.39.9000-16.fc41.aarch64 glibc-common-2.39.9000-16.fc41.aarch64 glibc-gconv-extra-2.39.9000-16.fc41.aarch64 glibc-minimal-langpack-2.39.9000-16.fc41.aarch64 gmp-1:6.3.0-1.fc41.aarch64 gnat-srpm-macros-6-5.fc40.noarch go-srpm-macros-3.6.0-1.fc41.noarch grep-3.11-7.fc40.aarch64 gzip-1.13-1.fc40.aarch64 info-7.1-2.fc40.aarch64 jansson-2.13.1-9.fc40.aarch64 kernel-srpm-macros-1.0-23.fc41.noarch keyutils-libs-1.6.3-3.fc40.aarch64 krb5-libs-1.21.2-5.fc40.aarch64 libacl-2.3.2-1.fc40.aarch64 libarchive-3.7.2-3.fc41.aarch64 libattr-2.5.2-3.fc40.aarch64 libblkid-2.40-13.fc41.aarch64 libbrotli-1.1.0-3.fc40.aarch64 libcap-2.69-8.fc41.aarch64 libcap-ng-0.8.5-1.fc41.aarch64 libcom_err-1.47.0-5.fc40.aarch64 libcurl-8.7.1-1.fc41.aarch64 libeconf-0.6.2-1.fc41.aarch64 libevent-2.1.12-12.fc40.aarch64 libfdisk-2.40-13.fc41.aarch64 libffi-3.4.6-1.fc41.aarch64 libgcc-14.0.1-0.15.fc41.aarch64 libgomp-14.0.1-0.15.fc41.aarch64 libidn2-2.3.7-1.fc40.aarch64 libmount-2.40-13.fc41.aarch64 libnghttp2-1.61.0-1.fc41.aarch64 libnsl2-2.0.1-1.fc40.aarch64 libpkgconf-2.1.0-1.fc40.aarch64 libpsl-0.21.5-3.fc40.aarch64 libpwquality-1.4.5-9.fc40.aarch64 libselinux-3.6-4.fc40.aarch64 libsemanage-3.6-3.fc40.aarch64 libsepol-3.6-3.fc40.aarch64 libsmartcols-2.40-13.fc41.aarch64 libssh-0.10.6-6.fc41.aarch64 libssh-config-0.10.6-6.fc41.noarch libstdc++-14.0.1-0.15.fc41.aarch64 libtasn1-4.19.0-6.fc40.aarch64 libtirpc-1.3.4-1.rc3.fc41.aarch64 libtool-ltdl-2.4.7-10.fc40.aarch64 libunistring-1.1-7.fc41.aarch64 libutempter-1.2.1-13.fc40.aarch64 libuuid-2.40-13.fc41.aarch64 libverto-0.3.2-8.fc40.aarch64 libxcrypt-4.4.36-5.fc40.aarch64 libxml2-2.12.6-1.fc41.aarch64 libzstd-1.5.6-1.fc41.aarch64 lua-libs-5.4.6-5.fc40.aarch64 lua-srpm-macros-1-13.fc40.noarch lz4-libs-1.9.4-6.fc40.aarch64 mpfr-4.2.1-3.fc40.aarch64 ncurses-base-6.4-12.20240127.fc40.noarch ncurses-libs-6.4-12.20240127.fc40.aarch64 ocaml-srpm-macros-9-3.fc40.noarch openblas-srpm-macros-2-17.fc41.noarch openldap-2.6.7-1.fc40.aarch64 openssl-libs-1:3.2.1-6.fc41.aarch64 p11-kit-0.25.3-4.fc40.aarch64 p11-kit-trust-0.25.3-4.fc40.aarch64 package-notes-srpm-macros-0.5-11.fc40.noarch pam-1.6.1-1.fc41.aarch64 pam-libs-1.6.1-1.fc41.aarch64 patch-2.7.6-24.fc40.aarch64 pcre2-10.43-1.fc41.aarch64 pcre2-syntax-10.43-1.fc41.noarch perl-srpm-macros-1-53.fc40.noarch pkgconf-2.1.0-1.fc40.aarch64 pkgconf-m4-2.1.0-1.fc40.noarch pkgconf-pkg-config-2.1.0-1.fc40.aarch64 popt-1.19-6.fc40.aarch64 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.aarch64 redhat-rpm-config-288-1.fc41.noarch rpm-4.19.1.1-1.fc40.aarch64 rpm-build-4.19.1.1-1.fc40.aarch64 rpm-build-libs-4.19.1.1-1.fc40.aarch64 rpm-libs-4.19.1.1-1.fc40.aarch64 rpm-sequoia-1.6.0-2.fc40.aarch64 rust-srpm-macros-26.2-1.fc41.noarch sed-4.9-1.fc40.aarch64 setup-2.14.5-2.fc40.noarch shadow-utils-2:4.15.1-2.fc41.aarch64 sqlite-libs-3.45.2-1.fc41.aarch64 systemd-libs-255.5-1.fc41.aarch64 tar-2:1.35-3.fc40.aarch64 unzip-6.0-63.fc40.aarch64 util-linux-2.40-13.fc41.aarch64 util-linux-core-2.40-13.fc41.aarch64 which-2.21-41.fc40.aarch64 xxhash-libs-0.8.2-2.fc40.aarch64 xz-1:5.4.6-3.fc41.aarch64 xz-libs-1:5.4.6-3.fc41.aarch64 zig-srpm-macros-1-2.fc40.noarch zip-3.0-40.fc40.aarch64 zlib-ng-compat-2.1.6-2.fc40.aarch64 zstd-1.5.6-1.fc41.aarch64 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.aarch64 ansible-srpm-macros-1-15.fc41.noarch audit-libs-4.0.1-1.fc41.aarch64 authselect-1.5.0-5.fc41.aarch64 authselect-libs-1.5.0-5.fc41.aarch64 basesystem-11-20.fc40.noarch bash-5.2.26-3.fc40.aarch64 binutils-2.42.50-6.fc41.aarch64 binutils-gold-2.42.50-6.fc41.aarch64 bzip2-1.0.8-18.fc40.aarch64 bzip2-libs-1.0.8-18.fc40.aarch64 ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch coreutils-9.5-1.fc41.aarch64 coreutils-common-9.5-1.fc41.aarch64 cpio-2.15-1.fc40.aarch64 cracklib-2.9.11-5.fc40.aarch64 crypto-policies-20240320-1.git58e3d95.fc41.noarch curl-8.7.1-1.fc41.aarch64 cyrus-sasl-lib-2.1.28-19.fc40.aarch64 debugedit-5.0-14.fc40.aarch64 diffutils-3.10-5.fc40.aarch64 dwz-0.15-6.fc40.aarch64 ed-1.20.2-1.fc41.aarch64 efi-srpm-macros-5-11.fc40.noarch elfutils-0.191-7.fc41.aarch64 elfutils-debuginfod-client-0.191-7.fc41.aarch64 elfutils-default-yama-scope-0.191-7.fc41.noarch elfutils-libelf-0.191-7.fc41.aarch64 elfutils-libs-0.191-7.fc41.aarch64 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.aarch64 file-libs-5.45-5.fc41.aarch64 filesystem-3.18-9.fc41.aarch64 findutils-4.9.0-8.fc40.aarch64 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.aarch64 gdb-minimal-14.2-5.fc41.aarch64 gdbm-1.23-6.fc40.aarch64 gdbm-libs-1.23-6.fc40.aarch64 ghc-srpm-macros-1.9.1-1.fc41.noarch glibc-2.39.9000-16.fc41.aarch64 glibc-common-2.39.9000-16.fc41.aarch64 glibc-gconv-extra-2.39.9000-16.fc41.aarch64 glibc-minimal-langpack-2.39.9000-16.fc41.aarch64 gmp-6.3.0-1.fc41.aarch64 gnat-srpm-macros-6-5.fc40.noarch go-srpm-macros-3.6.0-1.fc41.noarch grep-3.11-7.fc40.aarch64 gzip-1.13-1.fc40.aarch64 info-7.1-2.fc40.aarch64 jansson-2.13.1-9.fc40.aarch64 kernel-srpm-macros-1.0-23.fc41.noarch keyutils-libs-1.6.3-3.fc40.aarch64 krb5-libs-1.21.2-5.fc40.aarch64 libacl-2.3.2-1.fc40.aarch64 libarchive-3.7.2-3.fc41.aarch64 libattr-2.5.2-3.fc40.aarch64 libblkid-2.40-13.fc41.aarch64 libbrotli-1.1.0-3.fc40.aarch64 libcap-2.69-8.fc41.aarch64 libcap-ng-0.8.5-1.fc41.aarch64 libcom_err-1.47.0-5.fc40.aarch64 libcurl-8.7.1-1.fc41.aarch64 libeconf-0.6.2-1.fc41.aarch64 libevent-2.1.12-12.fc40.aarch64 libfdisk-2.40-13.fc41.aarch64 libffi-3.4.6-1.fc41.aarch64 libgcc-14.0.1-0.15.fc41.aarch64 libgomp-14.0.1-0.15.fc41.aarch64 libidn2-2.3.7-1.fc40.aarch64 libmount-2.40-13.fc41.aarch64 libnghttp2-1.61.0-1.fc41.aarch64 libnsl2-2.0.1-1.fc40.aarch64 libpkgconf-2.1.0-1.fc40.aarch64 libpsl-0.21.5-3.fc40.aarch64 libpwquality-1.4.5-9.fc40.aarch64 libselinux-3.6-4.fc40.aarch64 libsemanage-3.6-3.fc40.aarch64 libsepol-3.6-3.fc40.aarch64 libsmartcols-2.40-13.fc41.aarch64 libssh-0.10.6-6.fc41.aarch64 libssh-config-0.10.6-6.fc41.noarch libstdc++-14.0.1-0.15.fc41.aarch64 libtasn1-4.19.0-6.fc40.aarch64 libtirpc-1.3.4-1.rc3.fc41.aarch64 libtool-ltdl-2.4.7-10.fc40.aarch64 libunistring-1.1-7.fc41.aarch64 libutempter-1.2.1-13.fc40.aarch64 libuuid-2.40-13.fc41.aarch64 libverto-0.3.2-8.fc40.aarch64 libxcrypt-4.4.36-5.fc40.aarch64 libxml2-2.12.6-1.fc41.aarch64 libzstd-1.5.6-1.fc41.aarch64 lua-libs-5.4.6-5.fc40.aarch64 lua-srpm-macros-1-13.fc40.noarch lz4-libs-1.9.4-6.fc40.aarch64 mpfr-4.2.1-3.fc40.aarch64 ncurses-base-6.4-12.20240127.fc40.noarch ncurses-libs-6.4-12.20240127.fc40.aarch64 ocaml-srpm-macros-9-3.fc40.noarch openblas-srpm-macros-2-17.fc41.noarch openldap-2.6.7-1.fc40.aarch64 openssl-libs-3.2.1-6.fc41.aarch64 p11-kit-0.25.3-4.fc40.aarch64 p11-kit-trust-0.25.3-4.fc40.aarch64 package-notes-srpm-macros-0.5-11.fc40.noarch pam-1.6.1-1.fc41.aarch64 pam-libs-1.6.1-1.fc41.aarch64 patch-2.7.6-24.fc40.aarch64 pcre2-10.43-1.fc41.aarch64 pcre2-syntax-10.43-1.fc41.noarch perl-srpm-macros-1-53.fc40.noarch pkgconf-2.1.0-1.fc40.aarch64 pkgconf-m4-2.1.0-1.fc40.noarch pkgconf-pkg-config-2.1.0-1.fc40.aarch64 popt-1.19-6.fc40.aarch64 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.aarch64 redhat-rpm-config-288-1.fc41.noarch rpm-4.19.1.1-1.fc40.aarch64 rpm-build-4.19.1.1-1.fc40.aarch64 rpm-build-libs-4.19.1.1-1.fc40.aarch64 rpm-libs-4.19.1.1-1.fc40.aarch64 rpm-sequoia-1.6.0-2.fc40.aarch64 rust-srpm-macros-26.2-1.fc41.noarch sed-4.9-1.fc40.aarch64 setup-2.14.5-2.fc40.noarch shadow-utils-4.15.1-2.fc41.aarch64 sqlite-libs-3.45.2-1.fc41.aarch64 systemd-libs-255.5-1.fc41.aarch64 tar-1.35-3.fc40.aarch64 unzip-6.0-63.fc40.aarch64 util-linux-2.40-13.fc41.aarch64 util-linux-core-2.40-13.fc41.aarch64 which-2.21-41.fc40.aarch64 xxhash-libs-0.8.2-2.fc40.aarch64 xz-5.4.6-3.fc41.aarch64 xz-libs-5.4.6-3.fc41.aarch64 zig-srpm-macros-1-2.fc40.noarch zip-3.0-40.fc40.aarch64 zlib-ng-compat-2.1.6-2.fc40.aarch64 zstd-1.5.6-1.fc41.aarch64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1714089600 Wrote: /builddir/build/SRPMS/R-Rsamtools-2.18.0-1.fc41.src.rpm Finish: rpmbuild -bs cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-39-aarch64-1714176089.513502/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-aarch64-1714176089.513502/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-aarch64-1714176089.513502/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-aarch64-1714176089.513502/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-h4p4rxnq/R-Rsamtools/R-Rsamtools.spec) Config(child) 2 minutes 39 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-Rsamtools-2.18.0-1.fc41.src.rpm) Config(fedora-39-aarch64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-aarch64-bootstrap-1714176089.513502/root. INFO: reusing tmpfs at /var/lib/mock/fedora-39-aarch64-bootstrap-1714176089.513502/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-aarch64-1714176089.513502/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.aarch64 rpm-sequoia-1.6.0-1.fc39.aarch64 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-Rsamtools-2.18.0-1.fc41.src.rpm Start: build setup for R-Rsamtools-2.18.0-1.fc41.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1714089600 Wrote: /builddir/build/SRPMS/R-Rsamtools-2.18.0-1.fc41.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 48 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 58 kB/s | 3.8 kB 00:00 fedora 47 kB/s | 13 kB 00:00 updates 46 kB/s | 12 kB 00:00 Dependencies resolved. ====================================================================================================================================================== Package Arch Version Repository Size ====================================================================================================================================================== Installing: R-BiocGenerics noarch 0.42.0-8.fc41 copr_base 643 k R-BiocParallel aarch64 1.30.3-7.fc41 copr_base 1.5 M R-Biostrings-devel aarch64 2.64.1-8.fc41 copr_base 13 k R-GenomeInfoDb noarch 1.32.3-8.fc41 copr_base 3.8 M R-GenomicRanges aarch64 1.48.0-8.fc41 copr_base 2.0 M R-IRanges-devel aarch64 2.30.1-8.fc41 copr_base 11 k R-Rhtslib-devel aarch64 2.4.1-1.fc41 copr_base 593 k R-S4Vectors-devel aarch64 0.40.2-1.fc41 copr_base 14 k R-XVector-devel aarch64 0.42.0-1.fc41 copr_base 11 k R-bitops aarch64 1.0.7-12.fc41 copr_base 41 k R-core aarch64 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zlib-ng-compat-devel-2.1.6-2.fc40.aa 1.6 MB/s | 36 kB 00:00 -------------------------------------------------------------------------------- Total 57 MB/s | 543 MB 00:09 Running transaction check Transaction check succeeded. 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texlive-booktabs-11:svn53402-71.fc40.noarch texlive-breakurl-11:svn29901.1.40-71.fc40.noarch texlive-breqn-11:svn60881-71.fc40.noarch texlive-caption-11:svn66580-71.fc40.noarch texlive-carlisle-11:svn59577-71.fc40.noarch texlive-catchfile-11:svn53084-71.fc40.noarch texlive-changepage-11:svn15878.1.0c-71.fc40.noarch texlive-charter-11:svn15878.0-71.fc40.noarch texlive-cite-11:svn36428.5.5-71.fc40.noarch texlive-cm-11:svn57963-71.fc40.noarch texlive-cm-super-11:svn15878.0-71.fc40.noarch texlive-cmap-11:svn57640-71.fc40.noarch texlive-collection-basic-11:svn59159-71.fc40.noarch texlive-collection-latex-11:svn63515-71.fc40.noarch texlive-collection-latexrecommended-11:svn65512-71.fc40.noarch texlive-colorprofiles-11:svn49086-71.fc40.noarch texlive-colortbl-11:svn64015-71.fc40.noarch texlive-courier-11:svn61719-71.fc40.noarch texlive-crop-11:svn55424-71.fc40.noarch texlive-csquotes-11:svn64389-71.fc40.noarch texlive-ctable-11:svn38672-71.fc40.noarch texlive-ctablestack-11:svn38514-71.fc40.noarch texlive-currfile-11:svn64673-71.fc40.noarch texlive-dehyph-11:svn48599-71.fc40.noarch texlive-dvipdfmx-11:svn66203-84.fc41.aarch64 texlive-dvips-11:svn66203-84.fc41.aarch64 texlive-ec-11:svn25033.1.0-71.fc40.noarch texlive-enctex-11:svn34957.0-71.fc40.noarch texlive-enumitem-11:svn51423-71.fc40.noarch texlive-epstopdf-11:svn66461-84.fc41.noarch texlive-epstopdf-pkg-11:svn53546-71.fc40.noarch texlive-eso-pic-11:svn56658-71.fc40.noarch texlive-etex-11:svn66203-71.fc40.noarch texlive-etex-pkg-11:svn41784-71.fc40.noarch texlive-etexcmds-11:svn53171-71.fc40.noarch texlive-etoolbox-11:svn56554-71.fc40.noarch texlive-euenc-11:svn19795.0.1h-71.fc40.noarch texlive-euler-11:svn42428-71.fc40.noarch texlive-everysel-11:svn57489-71.fc40.noarch texlive-everyshi-11:svn57001-71.fc40.noarch texlive-extsizes-11:svn17263.1.4a-71.fc40.noarch texlive-fancybox-11:svn18304.1.4-71.fc40.noarch texlive-fancyhdr-11:svn64977-71.fc40.noarch texlive-fancyref-11:svn15878.0.9c-71.fc40.noarch texlive-fancyvrb-11:svn65585-71.fc40.noarch texlive-filecontents-11:svn52142-71.fc40.noarch texlive-filehook-11:svn64822-71.fc40.noarch texlive-finstrut-11:svn21719.0.5-71.fc40.noarch texlive-firstaid-11:svn64892-71.fc40.noarch texlive-fix2col-11:svn38770-71.fc40.noarch texlive-float-11:svn15878.1.3d-71.fc40.noarch texlive-fontspec-11:svn63386-71.fc40.noarch texlive-footmisc-11:svn62524-71.fc40.noarch texlive-footnotehyper-11:svn60374-71.fc40.noarch texlive-fp-11:svn49719-71.fc40.noarch texlive-fpl-11:svn54512-71.fc40.noarch texlive-geometry-11:svn61719-71.fc40.noarch texlive-gettitlestring-11:svn53170-71.fc40.noarch texlive-glyphlist-11:svn54074-84.fc41.noarch texlive-graphics-11:svn66204-71.fc40.noarch texlive-graphics-cfg-11:svn41448-71.fc40.noarch texlive-graphics-def-11:svn64487-71.fc40.noarch texlive-grfext-11:svn53024-71.fc40.noarch texlive-grffile-11:svn52756-71.fc40.noarch texlive-gsftopk-11:svn52851-84.fc41.aarch64 texlive-helvetic-11:svn61719-71.fc40.noarch texlive-hobsub-11:svn52810-71.fc40.noarch texlive-hologo-11:svn61719-71.fc40.noarch texlive-hopatch-11:svn65491-71.fc40.noarch texlive-hycolor-11:svn53584-71.fc40.noarch texlive-hypdoc-11:svn65678-71.fc40.noarch texlive-hyperref-11:svn65758-71.fc40.noarch texlive-hyph-utf8-11:svn61719-71.fc40.noarch texlive-hyphen-base-11:svn66413-71.fc40.noarch texlive-hyphenex-11:svn57387-71.fc40.noarch texlive-ifmtarg-11:svn47544-71.fc40.noarch texlive-ifplatform-11:svn45533-71.fc40.noarch texlive-iftex-11:svn61910-71.fc40.noarch texlive-index-11:svn24099.4.1beta-71.fc40.noarch texlive-infwarerr-11:svn53023-71.fc40.noarch texlive-intcalc-11:svn53168-71.fc40.noarch texlive-jknapltx-11:svn19440.0-71.fc40.noarch texlive-kastrup-11:svn15878.0-71.fc40.noarch texlive-knuth-lib-11:svn57963-71.fc40.noarch texlive-knuth-local-11:svn57963-71.fc40.noarch texlive-koma-script-11:svn64685-71.fc40.noarch texlive-kpathsea-11:svn66209-84.fc41.aarch64 texlive-kvdefinekeys-11:svn53193-71.fc40.noarch texlive-kvoptions-11:svn63622-71.fc40.noarch texlive-kvsetkeys-11:svn64632-71.fc40.noarch texlive-l3backend-11:svn65573-71.fc40.noarch texlive-l3experimental-11:svn65621-71.fc40.noarch texlive-l3kernel-11:svn66094-71.fc40.noarch texlive-l3packages-11:svn65722-71.fc40.noarch texlive-latex-11:svn65161-84.fc41.noarch texlive-latex-fonts-11:svn28888.0-71.fc40.noarch texlive-latex-lab-11:svn64892-71.fc40.noarch texlive-latexbug-11:svn63596-71.fc40.noarch texlive-latexconfig-11:svn53525-71.fc40.noarch texlive-letltxmacro-11:svn53022-71.fc40.noarch texlive-lib-11:20230311-84.fc41.aarch64 texlive-lineno-11:svn65586-71.fc40.noarch texlive-listings-11:svn66222-71.fc40.noarch texlive-lm-11:svn65956-71.fc40.noarch texlive-lm-math-11:svn36915.1.959-71.fc40.noarch texlive-logreq-11:svn53003-71.fc40.noarch texlive-ltabptch-11:svn17533.1.74d-71.fc40.noarch texlive-ltxcmds-11:svn56421-71.fc40.noarch texlive-ltxmisc-11:svn21927.0-71.fc40.noarch texlive-lua-alt-getopt-11:svn56414-71.fc40.noarch texlive-lua-uni-algos-11:svn62204-71.fc40.noarch texlive-luabidi-11:svn54512-71.fc40.noarch texlive-luahbtex-11:svn66186-84.fc41.aarch64 texlive-lualatex-math-11:svn61464-71.fc40.noarch texlive-lualibs-11:svn64615-71.fc40.noarch texlive-luaotfload-11:svn64616-84.fc41.noarch texlive-luatex-11:svn66967-84.fc41.aarch64 texlive-luatexbase-11:svn52663-71.fc40.noarch texlive-lwarp-11:svn66259-84.fc41.noarch texlive-makecmds-11:svn15878.0-71.fc40.noarch texlive-makeindex-11:svn62517-84.fc41.aarch64 texlive-marginnote-11:svn48383-71.fc40.noarch texlive-marvosym-11:svn29349.2.2a-71.fc40.noarch texlive-mathpazo-11:svn52663-71.fc40.noarch texlive-mathspec-11:svn42773-71.fc40.noarch texlive-mathtools-11:svn63767-71.fc40.noarch texlive-mdwtools-11:svn15878.1.05.4-71.fc40.noarch texlive-memoir-11:svn65040-71.fc40.noarch texlive-metafont-11:svn66186-84.fc41.aarch64 texlive-metalogo-11:svn18611.0.12-71.fc40.noarch texlive-mflogo-11:svn42428-71.fc40.noarch texlive-mfnfss-11:svn46036-71.fc40.noarch texlive-mfware-11:svn66186-84.fc41.aarch64 texlive-microtype-11:svn66587-71.fc40.noarch texlive-minitoc-11:svn61719-71.fc40.noarch texlive-mnsymbol-11:svn18651.1.4-71.fc40.noarch texlive-modes-11:svn61719-71.fc40.noarch texlive-mparhack-11:svn59066-71.fc40.noarch texlive-mptopdf-11:svn65952-84.fc41.noarch texlive-ms-11:svn57473-71.fc40.noarch texlive-multido-11:svn18302.1.42-71.fc40.noarch texlive-natbib-11:svn20668.8.31b-71.fc40.noarch texlive-newfloat-11:svn52906-71.fc40.noarch texlive-notoccite-11:svn18129.0-71.fc40.noarch texlive-ntgclass-11:svn65522-71.fc40.noarch texlive-oberdiek-11:svn65521-84.fc41.noarch texlive-pagesel-11:svn56105-71.fc40.noarch texlive-palatino-11:svn61719-71.fc40.noarch texlive-paralist-11:svn43021-71.fc40.noarch texlive-parallel-11:svn15878.0-71.fc40.noarch texlive-parskip-11:svn58358-71.fc40.noarch texlive-pdfcol-11:svn64469-71.fc40.noarch texlive-pdfcolfoot-11:svn65512-71.fc40.noarch texlive-pdfcolmk-11:svn52912-71.fc40.noarch texlive-pdfescape-11:svn53082-71.fc40.noarch texlive-pdflscape-11:svn64851-71.fc40.noarch texlive-pdfmanagement-testphase-11:svn66532-71.fc40.noarch texlive-pdfpages-11:svn65319-71.fc40.noarch texlive-pdftex-11:svn66243-84.fc41.aarch64 texlive-pdftexcmds-11:svn55777-71.fc40.noarch texlive-pgf-11:svn65553-71.fc40.noarch texlive-picture-11:svn54867-71.fc40.noarch texlive-placeins-11:svn19848.2.2-71.fc40.noarch texlive-plain-11:svn57963-71.fc40.noarch texlive-polyglossia-11:svn65792-71.fc40.noarch texlive-psfrag-11:svn15878.3.04-71.fc40.noarch texlive-pslatex-11:svn57434-71.fc40.noarch texlive-psnfss-11:svn54694-71.fc40.noarch texlive-pspicture-11:svn15878.0-71.fc40.noarch texlive-pst-3d-11:svn17257.1.10-71.fc40.noarch texlive-pst-coil-11:svn62977-71.fc40.noarch texlive-pst-eps-11:svn15878.1.0-71.fc40.noarch texlive-pst-fill-11:svn60671-71.fc40.noarch texlive-pst-grad-11:svn15878.1.06-71.fc40.noarch texlive-pst-math-11:svn64732-71.fc40.noarch texlive-pst-node-11:svn61838-71.fc40.noarch texlive-pst-ovl-11:svn54963-71.fc40.noarch texlive-pst-plot-11:svn65346-71.fc40.noarch texlive-pst-text-11:svn49542-71.fc40.noarch texlive-pst-tools-11:svn60621-71.fc40.noarch texlive-pst-tree-11:svn60421-71.fc40.noarch texlive-pstricks-11:svn65346-71.fc40.noarch texlive-pstricks-add-11:svn65067-71.fc40.noarch texlive-ragged2e-11:svn66152-71.fc40.noarch texlive-rcs-11:svn15878.0-71.fc40.noarch texlive-realscripts-11:svn56594-71.fc40.noarch texlive-refcount-11:svn53164-71.fc40.noarch texlive-rerunfilecheck-11:svn63869-71.fc40.noarch texlive-rsfs-11:svn15878.0-71.fc40.noarch texlive-sansmath-11:svn17997.1.1-71.fc40.noarch texlive-sansmathaccent-11:svn53628-71.fc40.noarch texlive-sauerj-11:svn15878.0-71.fc40.noarch texlive-section-11:svn20180.0-71.fc40.noarch texlive-seminar-11:svn59801-71.fc40.noarch texlive-sepnum-11:svn20186.2.0-71.fc40.noarch texlive-setspace-11:svn65206-71.fc40.noarch texlive-showexpl-11:svn57414-71.fc40.noarch texlive-stringenc-11:svn52982-71.fc40.noarch texlive-subfig-11:svn15878.1.3-71.fc40.noarch texlive-symbol-11:svn61719-71.fc40.noarch texlive-tex-11:svn66186-84.fc41.aarch64 texlive-tex-ini-files-11:svn40533-71.fc40.noarch texlive-texlive-common-doc-11:svn54176-71.fc40.noarch texlive-texlive-en-11:svn66572-84.fc41.noarch texlive-texlive-msg-translations-11:svn66593-71.fc40.noarch texlive-texlive-scripts-11:svn66584-84.fc41.noarch texlive-texlive.infra-11:svn66512-84.fc41.noarch texlive-textcase-11:svn63868-71.fc40.noarch texlive-thumbpdf-11:svn62518-84.fc41.noarch texlive-times-11:svn61719-71.fc40.noarch texlive-tipa-11:svn29349.1.3-71.fc40.noarch texlive-titlesec-11:svn59845-71.fc40.noarch texlive-tools-11:svn64892-71.fc40.noarch texlive-translator-11:svn59412-71.fc40.noarch texlive-transparent-11:svn64852-71.fc40.noarch texlive-typehtml-11:svn17134.0-71.fc40.noarch texlive-ucharcat-11:svn38907-71.fc40.noarch texlive-ucs-11:svn64114-71.fc40.noarch texlive-underscore-11:svn18261.0-71.fc40.noarch texlive-unicode-data-11:svn64423-71.fc40.noarch texlive-unicode-math-11:svn61719-71.fc40.noarch texlive-uniquecounter-11:svn53162-71.fc40.noarch texlive-url-11:svn32528.3.4-71.fc40.noarch texlive-utopia-11:svn15878.0-71.fc40.noarch texlive-varwidth-11:svn24104.0.92-71.fc40.noarch texlive-xcolor-11:svn63563-71.fc40.noarch texlive-xdvi-11:svn62387-84.fc41.aarch64 texlive-xetex-11:svn66203-84.fc41.aarch64 texlive-xetexconfig-11:svn45845-71.fc40.noarch texlive-xifthen-11:svn38929-71.fc40.noarch texlive-xkeyval-11:svn63616-71.fc40.noarch texlive-xltxtra-11:svn56594-71.fc40.noarch texlive-xpatch-11:svn54563-71.fc40.noarch texlive-xstring-11:svn65551-71.fc40.noarch texlive-xunicode-11:svn30466.0.981-71.fc40.noarch texlive-zapfding-11:svn61719-71.fc40.noarch texlive-zref-11:svn62977-71.fc40.noarch tk-1:8.6.14-1.fc41.aarch64 tk-devel-1:8.6.14-1.fc41.aarch64 tre-0.8.0-43.20140228gitc2f5d13.fc40.aarch64 tre-common-0.8.0-43.20140228gitc2f5d13.fc40.noarch tre-devel-0.8.0-43.20140228gitc2f5d13.fc40.aarch64 ttmkfdir-3.0.9-70.fc40.aarch64 tzdata-2024a-5.fc41.noarch tzdata-java-2024a-5.fc41.noarch urw-base35-bookman-fonts-20200910-20.fc41.noarch urw-base35-c059-fonts-20200910-20.fc41.noarch urw-base35-d050000l-fonts-20200910-20.fc41.noarch urw-base35-fonts-20200910-20.fc41.noarch urw-base35-fonts-common-20200910-20.fc41.noarch urw-base35-gothic-fonts-20200910-20.fc41.noarch urw-base35-nimbus-mono-ps-fonts-20200910-20.fc41.noarch urw-base35-nimbus-roman-fonts-20200910-20.fc41.noarch urw-base35-nimbus-sans-fonts-20200910-20.fc41.noarch urw-base35-p052-fonts-20200910-20.fc41.noarch urw-base35-standard-symbols-ps-fonts-20200910-20.fc41.noarch urw-base35-z003-fonts-20200910-20.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 xpdf-libs-1:4.05-3.fc41.aarch64 xz-devel-1:5.4.6-3.fc41.aarch64 zlib-ng-compat-devel-2.1.6-2.fc40.aarch64 zziplib-0.13.72-6.fc40.aarch64 Complete! Finish: build setup for R-Rsamtools-2.18.0-1.fc41.src.rpm Start: rpmbuild R-Rsamtools-2.18.0-1.fc41.src.rpm Building target platforms: aarch64 Building for target aarch64 setting SOURCE_DATE_EPOCH=1714089600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.KEgHL5 + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf Rsamtools + /usr/bin/mkdir -p Rsamtools + cd Rsamtools + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/Rsamtools_2.18.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + rm -rf /builddir/build/BUILD/Rsamtools-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/Rsamtools-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + pushd Rsamtools ~/build/BUILD/Rsamtools/Rsamtools ~/build/BUILD/Rsamtools Patch #0 (0001-format-security-fix.patch): + echo 'Patch #0 (0001-format-security-fix.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file src/samtools_patch.c patching file src/zip_compression.c + popd ~/build/BUILD/Rsamtools + sed -i 's|zlibbioc, ||g' Rsamtools/DESCRIPTION + sed -i '/import(zlibbioc)/d' Rsamtools/NAMESPACE + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.4iMH9Z + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-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 Rsamtools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.k9Qacl + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-Rsamtools-2.18.0-1.fc41.aarch64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-Rsamtools-2.18.0-1.fc41.aarch64 ++ dirname /builddir/build/BUILDROOT/R-Rsamtools-2.18.0-1.fc41.aarch64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-Rsamtools-2.18.0-1.fc41.aarch64 + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-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 Rsamtools + mkdir -p /builddir/build/BUILDROOT/R-Rsamtools-2.18.0-1.fc41.aarch64/usr/lib64/R/library + R CMD INSTALL -l /builddir/build/BUILDROOT/R-Rsamtools-2.18.0-1.fc41.aarch64/usr/lib64/R/library Rsamtools * installing *source* package ‘Rsamtools’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 14.0.1 20240411 (Red Hat 14.0.1-0)’ using C++ compiler: ‘g++ (GCC) 14.0.1 20240411 (Red Hat 14.0.1-0)’ gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c IRanges_stubs.c -o IRanges_stubs.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c PileupBuffer.cpp -o PileupBuffer.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c PosCacheColl.cpp -o PosCacheColl.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c R_init_Rsamtools.c -o R_init_Rsamtools.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c ResultManager.cpp -o ResultManager.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c XVector_stubs.c -o XVector_stubs.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c as_bam.c -o as_bam.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c bam_data.c -o bam_data.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c bam_mate_iter.cpp -o bam_mate_iter.o In file included from Template.h:9, from BamIterator.h:10, from BamRangeIterator.h:7, from bam_mate_iter.cpp:2: BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’: /usr/lib64/R/library/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) | ~~~~~~~~~^~~~~~~~~~~~~~ BamRangeIterator.h:138:16: note: in expansion of macro ‘bam_seek’ 138 | (void) bam_seek(bfile, pos, SEEK_SET); | ^~~~~~~~ BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’: /usr/lib64/R/library/Rhtslib/include/samtools-1.7-compat.h:14:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) | ~~~~~~~~~^~~~~~~~~~~~~~ BamIterator.h:87:16: note: in expansion of macro ‘bam_seek’ 87 | (void) bam_seek(bfile, 0, 0); | ^~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c bam_plbuf.c -o bam_plbuf.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c bam_sort.c -o bam_sort.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c bambuffer.c -o bambuffer.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c bamfile.c -o bamfile.o bamfile.c: In function ‘bamfile_isincomplete’: bamfile.c:168:20: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 168 | (void) bgzf_seek(bfile->file->x.bam, offset, SEEK_SET); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘_bam_tryindexload’, inlined from ‘_bamfile_open_r’ at bamfile.c:89:24, inlined from ‘bamfile_open’ at bamfile.c:127:17: bamfile.c:29:17: warning: ‘cfile’ may be used uninitialized [-Wmaybe-uninitialized] 29 | index = hts_idx_load2(file, indexname); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bamfile.c: In function ‘bamfile_open’: bamfile.c:73:17: note: ‘cfile’ was declared here 73 | const char *cfile; | ^~~~~ gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c bcffile.c -o bcffile.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c bedidx.c -o bedidx.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c encode.c -o encode.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c fafile.c -o fafile.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c idxstats.c -o idxstats.o In file included from bamfile.h:5, from idxstats.c:1: idxstats.c: In function ‘idxstats_bamfile’: /usr/lib64/R/library/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) | ^~~~~~~~~~~~~~~~~~~~~~~ idxstats.c:20:12: note: in expansion of macro ‘bam_seek’ 20 | (void) bam_seek(fp, 0, 0); | ^~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c io_sam.c -o io_sam.o In file included from io_sam.c:2: io_sam.c: In function ‘_scan_bam_all’: /usr/lib64/R/library/Rhtslib/include/samtools-1.7-compat.h:14:32: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir) | ^~~~~~~~~~~~~~~~~~~~~~~ io_sam.c:307:12: note: in expansion of macro ‘bam_seek’ 307 | (void) bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET); | ^~~~~~~~ g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o g++ -std=gnu++17 -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c pileup.cpp -o pileup.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c pileupbam.c -o pileupbam.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c sam_opts.c -o sam_opts.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c sam_utils.c -o sam_utils.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c samtools_patch.c -o samtools_patch.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c scan_bam_data.c -o scan_bam_data.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c tabixfile.c -o tabixfile.o tabixfile.c: In function ‘index_tabix’: tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations] 190 | if (bgzf_is_bgzf(fn) != 1) | ^~ In file included from tabixfile.c:3: /usr/lib64/R/library/Rhtslib/include/htslib/bgzf.h:270:9: note: declared here 270 | int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead"); | ^~~~~~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c tagfilter.c -o tagfilter.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c utilities.c -o utilities.o gcc -I"/usr/include/R" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib64/R/library/Rhtslib/include' -I'/usr/lib64/R/library/S4Vectors/include' -I'/usr/lib64/R/library/IRanges/include' -I'/usr/lib64/R/library/XVector/include' -I'/usr/lib64/R/library/Biostrings/include' -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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c zip_compression.c -o zip_compression.o g++ -std=gnu++17 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -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 Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o bedidx.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o /usr/lib64/R/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILDROOT/R-Rsamtools-2.18.0-1.fc41.aarch64/usr/lib64/R/library/00LOCK-Rsamtools/00new/Rsamtools/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘Rsamtools’ finding HTML links ... done ApplyPileupsParam-class html BamFile-class html finding level-2 HTML links ... done BamViews-class html BcfFile-class html FaFile-class html PileupFiles-class html Rsamtools-package html RsamtoolsFile-class html RsamtoolsFileList-class html ScanBamParam-class html ScanBcfParam-class html TabixFile-class html applyPileups html defunct html deprecated html headerTabix html indexTabix html pileup html quickBamFlagSummary html readPileup html scanBam html scanBcf html scanFa html scanTabix html seqnamesTabix html testPairedEndBam html zip html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rsamtools) + test -d Rsamtools/src + cd Rsamtools/src + rm -f Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o bedidx.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o Rsamtools.so + rm -f /builddir/build/BUILDROOT/R-Rsamtools-2.18.0-1.fc41.aarch64/usr/lib64/R/library/R.css + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 2.18.0-1.fc41 --unique-debug-suffix -2.18.0-1.fc41.aarch64 --unique-debug-src-base R-Rsamtools-2.18.0-1.fc41.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/Rsamtools find-debuginfo: starting Extracting debug info from 1 files DWARF-compressing 1 files sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/R-Rsamtools-2.18.0-1.fc41.aarch64 488 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs mangling shebang in /usr/lib64/R/library/Rsamtools/scripts/update-samtools.sh from /bin/sh to #!/usr/bin/sh + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.R0gUq8 + 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 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-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 Rsamtools + RPM_EC=0 ++ jobs -p + exit 0 Processing files: R-Rsamtools-2.18.0-1.fc41.aarch64 Provides: R(Rsamtools) = 2.18.0 R-Rsamtools = 2.18.0-1.fc41 R-Rsamtools(aarch-64) = 2.18.0-1.fc41 R-Rsamtools-devel = 2.18.0-1.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/sh R(ABI) = 4.4 R(BiocGenerics) >= 0.25.1 R(BiocParallel) R(Biostrings) >= 2.47.6 R(GenomeInfoDb) >= 1.1.3 R(GenomicRanges) >= 1.31.8 R(IRanges) >= 2.13.12 R(S4Vectors) >= 0.17.25 R(XVector) >= 0.19.7 R(bitops) R(methods) R(stats) R(utils) R-core >= 3.5.0 ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libR.so()(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libcurl.so.4()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.3.3)(64bit) rtld(GNU_HASH) Obsoletes: R-Rsamtools-devel <= 1.34.1 Suggests: R(GenomicAlignments) R(RUnit) R(knitr) Processing files: R-Rsamtools-debugsource-2.18.0-1.fc41.aarch64 Provides: R-Rsamtools-debugsource = 2.18.0-1.fc41 R-Rsamtools-debugsource(aarch-64) = 2.18.0-1.fc41 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-Rsamtools-debuginfo-2.18.0-1.fc41.aarch64 Provides: R-Rsamtools-debuginfo = 2.18.0-1.fc41 R-Rsamtools-debuginfo(aarch-64) = 2.18.0-1.fc41 debuginfo(build-id) = 30a99b737362cb2e927acc3d36392eb76c197127 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-Rsamtools-debugsource(aarch-64) = 2.18.0-1.fc41 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-Rsamtools-2.18.0-1.fc41.aarch64 Wrote: /builddir/build/RPMS/R-Rsamtools-debugsource-2.18.0-1.fc41.aarch64.rpm Wrote: /builddir/build/RPMS/R-Rsamtools-debuginfo-2.18.0-1.fc41.aarch64.rpm Wrote: /builddir/build/RPMS/R-Rsamtools-2.18.0-1.fc41.aarch64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.I4z4Mo + umask 022 + cd /builddir/build/BUILD + cd Rsamtools + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-Rsamtools-2.18.0-1.fc41.aarch64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.j70Fmw + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/Rsamtools-SPECPARTS + rm -rf Rsamtools Rsamtools.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild R-Rsamtools-2.18.0-1.fc41.src.rpm Finish: build phase for R-Rsamtools-2.18.0-1.fc41.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-aarch64-1714176089.513502/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-aarch64-1714176089.513502/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-aarch64-1714176089.513502/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/R-Rsamtools-2.18.0-1.fc41.src.rpm) Config(child) 2 minutes 2 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-Rsamtools-debuginfo", "epoch": null, "version": "2.18.0", "release": "1.fc41", "arch": "aarch64" }, { "name": "R-Rsamtools", "epoch": null, "version": "2.18.0", "release": "1.fc41", "arch": "src" }, { "name": "R-Rsamtools-debugsource", "epoch": null, "version": "2.18.0", "release": "1.fc41", "arch": "aarch64" }, { "name": "R-Rsamtools", "epoch": null, "version": "2.18.0", "release": "1.fc41", "arch": "aarch64" } ] } RPMResults finished