Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c119' (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/6916653-fedora-39-x86_64 --chroot fedora-39-x86_64 Version: 0.70 PID: 6374 Logging PID: 6375 Task: {'appstream': False, 'background': True, 'build_id': 6916653, 'buildroot_pkgs': [], 'chroot': 'fedora-39-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '9dc77ce638757bc9ecf31a5ec05284fd37bf486c', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/scipy-1.10.0/snakemake', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'snakemake', 'package_version': '8.1.2-2', 'project_dirname': 'scipy-1.10.0', 'project_name': 'scipy-1.10.0', 'project_owner': 'psimovec', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/psimovec/scipy-1.10.0/fedora-39-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}, {'baseurl': 'http://kojipkgs.fedoraproject.org/repos/rawhide/latest/$basearch/', 'id': 'http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch', 'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch'}], 'sandbox': 'psimovec/scipy-1.10.0--https://src.fedoraproject.org/user/music', 'source_json': {}, 'source_type': None, 'submitter': 'https://src.fedoraproject.org/user/music', 'tags': [], 'task_id': '6916653-fedora-39-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/psimovec/scipy-1.10.0/snakemake /var/lib/copr-rpmbuild/workspace/workdir-8xe39ldh/snakemake --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/scipy-1.10.0/snakemake', '/var/lib/copr-rpmbuild/workspace/workdir-8xe39ldh/snakemake', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-8xe39ldh/snakemake'... Running: git checkout 9dc77ce638757bc9ecf31a5ec05284fd37bf486c -- cmd: ['git', 'checkout', '9dc77ce638757bc9ecf31a5ec05284fd37bf486c', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-8xe39ldh/snakemake rc: 0 stdout: stderr: Note: switching to '9dc77ce638757bc9ecf31a5ec05284fd37bf486c'. 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 9dc77ce automatic import of snakemake Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-8xe39ldh/snakemake 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 snakemake-8.1.2.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o snakemake-8.1.2.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/psimovec/scipy-1.10.0/snakemake/snakemake-8.1.2.tar.gz/md5/a4c5ca0b13d107d44775e40f3a4c625f/snakemake-8.1.2.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 8425k 100 8425k 0 0 37.4M 0 --:--:-- --:--:-- --:--:-- 37.5M INFO: Reading stdout from command: md5sum snakemake-8.1.2.tar.gz /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-8xe39ldh/snakemake/snakemake.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-8xe39ldh/snakemake --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1705640458.173212 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.4 starting (python version = 3.11.3, NVR = mock-5.4-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-8xe39ldh/snakemake/snakemake.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-8xe39ldh/snakemake --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1705640458.173212 -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-8xe39ldh/snakemake/snakemake.spec) Config(fedora-39-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.4 INFO: Mock Version: 5.4 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1705640458.173212/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:39 INFO: Pulling image: registry.fedoraproject.org/fedora:39 INFO: Copy content of container registry.fedoraproject.org/fedora:39 to /var/lib/mock/fedora-39-x86_64-bootstrap-1705640458.173212/root INFO: Checking that registry.fedoraproject.org/fedora:39 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:39 with podman image mount INFO: image registry.fedoraproject.org/fedora:39 as /var/lib/containers/storage/overlay/8ff7ad910417a7b8a49019008335921d2aac0e3304a19ce258deabf431e59801/merged INFO: umounting image registry.fedoraproject.org/fedora:39 (/var/lib/containers/storage/overlay/8ff7ad910417a7b8a49019008335921d2aac0e3304a19ce258deabf431e59801/merged) with podman image umount INFO: Package manager dnf detected and used (fallback) INFO: Bootstrap image not marked ready Start(bootstrap): installing dnf tooling No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 11 MB/s | 2.1 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 41 MB/s | 72 MB 00:01 fedora 23 MB/s | 89 MB 00:03 updates 13 MB/s | 28 MB 00:02 Last metadata expiration check: 0:00:01 ago on Fri Jan 19 05:01:48 2024. Package python3-dnf-4.18.1-2.fc39.noarch is already installed. Dependencies resolved. ========================================================================================================================= Package Arch Version Repository Size ========================================================================================================================= Installing: python3-dnf-plugins-core noarch 4.4.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 302 k Upgrading: dnf noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 496 k dnf-data noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k python3-dnf noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 549 k yum noarch 4.18.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k Installing dependencies: dbus-libs x86_64 1:1.14.10-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 155 k python3-dateutil noarch 1:2.8.2-11.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 345 k python3-dbus x86_64 1.3.2-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 146 k python3-distro noarch 1.9.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 45 k python3-six noarch 1.16.0-12.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k python3-systemd x86_64 235-5.fc39 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): dbus-libs-1.14.10-1.fc40.x86_64.rpm 715 kB/s | 155 kB 00:00 (2/11): python3-dbus-1.3.2-4.fc39.x86_64.rpm 632 kB/s | 146 kB 00:00 (3/11): python3-dateutil-2.8.2-11.fc40.noarch.r 1.3 MB/s | 345 kB 00:00 (4/11): python3-distro-1.9.0-1.fc40.noarch.rpm 797 kB/s | 45 kB 00:00 (5/11): python3-dnf-plugins-core-4.4.4-1.fc40.n 3.3 MB/s | 302 kB 00:00 (6/11): python3-systemd-235-5.fc39.x86_64.rpm 1.6 MB/s | 101 kB 00:00 (7/11): dnf-data-4.18.2-1.fc40.noarch.rpm 683 kB/s | 39 kB 00:00 (8/11): dnf-4.18.2-1.fc40.noarch.rpm 4.2 MB/s | 496 kB 00:00 (9/11): yum-4.18.2-1.fc40.noarch.rpm 436 kB/s | 37 kB 00:00 (10/11): python3-dnf-4.18.2-1.fc40.noarch.rpm 3.4 MB/s | 549 kB 00:00 (11/11): python3-six-1.16.0-12.fc39.noarch.rpm 134 kB/s | 41 kB 00:00 -------------------------------------------------------------------------------- Total 3.9 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-4.18.2-1.fc40.noarch 1/15 Upgrading : python3-dnf-4.18.2-1.fc40.noarch 2/15 Upgrading : dnf-4.18.2-1.fc40.noarch 3/15 Running scriptlet: dnf-4.18.2-1.fc40.noarch 3/15 Installing : python3-systemd-235-5.fc39.x86_64 4/15 Installing : python3-six-1.16.0-12.fc39.noarch 5/15 Installing : python3-dateutil-1:2.8.2-11.fc40.noarch 6/15 Installing : python3-distro-1.9.0-1.fc40.noarch 7/15 Installing : dbus-libs-1:1.14.10-1.fc40.x86_64 8/15 Installing : python3-dbus-1.3.2-4.fc39.x86_64 9/15 Installing : python3-dnf-plugins-core-4.4.4-1.fc40.noarch 10/15 Upgrading : yum-4.18.2-1.fc40.noarch 11/15 Cleanup : yum-4.18.1-2.fc39.noarch 12/15 Running scriptlet: dnf-4.18.1-2.fc39.noarch 13/15 Cleanup : dnf-4.18.1-2.fc39.noarch 13/15 Running scriptlet: dnf-4.18.1-2.fc39.noarch 13/15 Cleanup : python3-dnf-4.18.1-2.fc39.noarch 14/15 Cleanup : dnf-data-4.18.1-2.fc39.noarch 15/15 Running scriptlet: dnf-data-4.18.1-2.fc39.noarch 15/15 Verifying : dbus-libs-1:1.14.10-1.fc40.x86_64 1/15 Verifying : python3-dateutil-1:2.8.2-11.fc40.noarch 2/15 Verifying : python3-dbus-1.3.2-4.fc39.x86_64 3/15 Verifying : python3-distro-1.9.0-1.fc40.noarch 4/15 Verifying : python3-dnf-plugins-core-4.4.4-1.fc40.noarch 5/15 Verifying : python3-six-1.16.0-12.fc39.noarch 6/15 Verifying : python3-systemd-235-5.fc39.x86_64 7/15 Verifying : dnf-4.18.2-1.fc40.noarch 8/15 Verifying : dnf-4.18.1-2.fc39.noarch 9/15 Verifying : dnf-data-4.18.2-1.fc40.noarch 10/15 Verifying : dnf-data-4.18.1-2.fc39.noarch 11/15 Verifying : python3-dnf-4.18.2-1.fc40.noarch 12/15 Verifying : python3-dnf-4.18.1-2.fc39.noarch 13/15 Verifying : yum-4.18.2-1.fc40.noarch 14/15 Verifying : yum-4.18.1-2.fc39.noarch 15/15 Upgraded: dnf-4.18.2-1.fc40.noarch dnf-data-4.18.2-1.fc40.noarch python3-dnf-4.18.2-1.fc40.noarch yum-4.18.2-1.fc40.noarch Installed: dbus-libs-1:1.14.10-1.fc40.x86_64 python3-dateutil-1:2.8.2-11.fc40.noarch python3-dbus-1.3.2-4.fc39.x86_64 python3-distro-1.9.0-1.fc40.noarch python3-dnf-plugins-core-4.4.4-1.fc40.noarch python3-six-1.16.0-12.fc39.noarch python3-systemd-235-5.fc39.x86_64 Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1705640458.173212/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-4.19.0-1.fc39.x86_64 rpm-sequoia-1.5.0-1.fc39.x86_64 python3-dnf-4.18.2-1.fc40.noarch python3-dnf-plugins-core-4.4.4-1.fc40.noarch yum-4.18.2-1.fc40.noarch Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 5.4 MB/s | 2.1 MB 00:00 Additional repo http_kojipkgs_fedoraproject_org 41 MB/s | 72 MB 00:01 fedora 20 MB/s | 89 MB 00:04 updates 18 MB/s | 28 MB 00:01 Dependencies resolved. ======================================================================================================================================== Package Arch Version Repository Size ======================================================================================================================================== Installing group/module packages: bash x86_64 5.2.21-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 M bzip2 x86_64 1.0.8-16.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 52 k coreutils x86_64 9.4-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M cpio x86_64 2.14-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 273 k diffutils x86_64 3.10-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 390 k fedora-release-common noarch 40-0.29 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k findutils x86_64 1:4.9.0-6.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 482 k gawk x86_64 5.3.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M glibc-minimal-langpack x86_64 2.38.9000-33.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 95 k grep x86_64 3.11-5.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 287 k gzip x86_64 1.12-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 159 k info x86_64 7.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 184 k patch x86_64 2.7.6-22.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 125 k redhat-rpm-config noarch 280-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 75 k rpm-build x86_64 4.19.1-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 72 k sed x86_64 4.8-14.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 297 k shadow-utils x86_64 2:4.14.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.2 M tar x86_64 2:1.35-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 855 k unzip x86_64 6.0-62.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 184 k util-linux x86_64 2.39.3-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.1 M which x86_64 2.21-40.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 42 k xz x86_64 5.4.5-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 531 k Installing dependencies: alternatives x86_64 1.26-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40 k ansible-srpm-macros noarch 1-12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k audit-libs x86_64 4.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 120 k authselect x86_64 1.5.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 144 k authselect-libs x86_64 1.5.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 234 k basesystem noarch 11-18.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 7.2 k binutils x86_64 2.41-26.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 6.2 M binutils-gold x86_64 2.41-26.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 780 k bzip2-libs x86_64 1.0.8-16.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 41 k ca-certificates noarch 2023.2.62_v7.0.401-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 863 k coreutils-common x86_64 9.4-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.1 M cracklib x86_64 2.9.11-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 83 k crypto-policies noarch 20231204-1.git1e3a2e4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 69 k curl x86_64 8.5.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 373 k cyrus-sasl-lib x86_64 2.1.28-17.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 789 k debugedit x86_64 5.0-12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 78 k dwz x86_64 0.15-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 134 k ed x86_64 1.19-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 79 k efi-srpm-macros noarch 5-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 22 k elfutils x86_64 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 545 k elfutils-debuginfod-client x86_64 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 38 k elfutils-default-yama-scope noarch 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 13 k elfutils-libelf x86_64 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 194 k elfutils-libs x86_64 0.190-4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 259 k fedora-gpg-keys noarch 40-0.2 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 119 k fedora-release noarch 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00:00 (62/152): krb5-libs-1.21.2-3.fc40.x86_64.rpm 7.1 MB/s | 751 kB 00:00 (63/152): libattr-2.5.2-1.fc40.x86_64.rpm 251 kB/s | 18 kB 00:00 (64/152): libblkid-2.39.3-2.fc40.x86_64.rpm 1.6 MB/s | 114 kB 00:00 (65/152): libarchive-3.7.2-1.fc40.x86_64.rpm 2.2 MB/s | 408 kB 00:00 (66/152): libbrotli-1.1.0-1.fc40.x86_64.rpm 4.2 MB/s | 336 kB 00:00 (67/152): libcap-2.69-1.fc40.x86_64.rpm 1.5 MB/s | 83 kB 00:00 (68/152): libcap-ng-0.8.4-2.fc40.x86_64.rpm 725 kB/s | 33 kB 00:00 (69/152): libcom_err-1.47.0-2.fc39.x86_64.rpm 481 kB/s | 26 kB 00:00 (70/152): libcurl-8.5.0-1.fc40.x86_64.rpm 5.8 MB/s | 345 kB 00:00 (71/152): libeconf-0.5.2-1.fc40.x86_64.rpm 522 kB/s | 30 kB 00:00 (72/152): libfdisk-2.39.3-2.fc40.x86_64.rpm 3.2 MB/s | 160 kB 00:00 (73/152): libffi-3.4.4-5.fc40.x86_64.rpm 684 kB/s | 39 kB 00:00 (74/152): libevent-2.1.12-9.fc39.x86_64.rpm 2.2 MB/s | 258 kB 00:00 (75/152): libgcc-14.0.1-0.1.fc40.x86_64.rpm 1.1 MB/s | 109 kB 00:00 (76/152): libgomp-14.0.1-0.1.fc40.x86_64.rpm 2.5 MB/s | 326 kB 00:00 (77/152): libidn2-2.3.4-3.fc39.x86_64.rpm 898 kB/s | 111 kB 00:00 (78/152): libmount-2.39.3-2.fc40.x86_64.rpm 2.0 MB/s | 153 kB 00:00 (79/152): libnghttp2-1.58.0-1.fc40.x86_64.rpm 1.4 MB/s | 76 kB 00:00 (80/152): libnsl2-2.0.0-6.fc39.x86_64.rpm 612 kB/s | 30 kB 00:00 (81/152): libpkgconf-1.9.5-2.fc39.x86_64.rpm 720 kB/s | 38 kB 00:00 (82/152): libpsl-0.21.5-1.fc40.x86_64.rpm 1.0 MB/s | 63 kB 00:00 (83/152): libpwquality-1.4.5-6.fc39.x86_64.rpm 1.8 MB/s | 108 kB 00:00 (84/152): libselinux-3.6-2.fc40.x86_64.rpm 1.5 MB/s | 88 kB 00:00 (85/152): libsemanage-3.6-1.fc40.x86_64.rpm 2.4 MB/s | 116 kB 00:00 (86/152): libsmartcols-2.39.3-2.fc40.x86_64.rpm 1.5 MB/s | 67 kB 00:00 (87/152): libsepol-3.6-1.fc40.x86_64.rpm 5.1 MB/s | 340 kB 00:00 (88/152): libssh-0.10.6-2.fc40.x86_64.rpm 5.5 MB/s | 213 kB 00:00 (89/152): libssh-config-0.10.6-2.fc40.noarch.rp 270 kB/s | 9.1 kB 00:00 (90/152): libtasn1-4.19.0-3.fc39.x86_64.rpm 1.8 MB/s | 74 kB 00:00 (91/152): 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00:00 (149/152): zig-srpm-macros-1-1.fc40.noarch.rpm 152 kB/s | 8.0 kB 00:00 (150/152): zlib-ng-compat-2.1.6-1.fc40.x86_64.r 1.5 MB/s | 76 kB 00:00 (151/152): zip-3.0-39.fc40.x86_64.rpm 3.0 MB/s | 266 kB 00:00 (152/152): zstd-1.5.5-4.fc39.x86_64.rpm 3.4 MB/s | 482 kB 00:00 -------------------------------------------------------------------------------- Total 9.5 MB/s | 52 MB 00:05 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-6.fc39.x86_64 1/1 Preparing : 1/1 Installing : libgcc-14.0.1-0.1.fc40.x86_64 1/152 Running scriptlet: libgcc-14.0.1-0.1.fc40.x86_64 1/152 Installing : crypto-policies-20231204-1.git1e3a2e4.fc40.noarc 2/152 Running scriptlet: crypto-policies-20231204-1.git1e3a2e4.fc40.noarc 2/152 Installing : fedora-release-identity-basic-40-0.29.noarch 3/152 Installing : fedora-repos-rawhide-40-0.2.noarch 4/152 Installing : fedora-gpg-keys-40-0.2.noarch 5/152 Installing : fedora-repos-40-0.2.noarch 6/152 Installing : fedora-release-common-40-0.29.noarch 7/152 Installing : fedora-release-40-0.29.noarch 8/152 Installing : setup-2.14.5-1.fc40.noarch 9/152 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.14.5-1.fc40.noarch 9/152 Installing : filesystem-3.18-6.fc39.x86_64 10/152 Installing : basesystem-11-18.fc39.noarch 11/152 Installing : rust-srpm-macros-25.2-2.fc40.noarch 12/152 Installing : 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Installing : cracklib-2.9.11-2.fc39.x86_64 117/152 Installing : libpwquality-1.4.5-6.fc39.x86_64 118/152 Installing : authselect-1.5.0-1.fc40.x86_64 119/152 Installing : libnsl2-2.0.0-6.fc39.x86_64 120/152 Installing : pam-1.5.3-9.fc40.x86_64 121/152 Installing : libssh-0.10.6-2.fc40.x86_64 122/152 Installing : libarchive-3.7.2-1.fc40.x86_64 123/152 Installing : libevent-2.1.12-9.fc39.x86_64 124/152 Installing : openldap-2.6.6-1.fc39.x86_64 125/152 Installing : libcurl-8.5.0-1.fc40.x86_64 126/152 Installing : elfutils-libs-0.190-4.fc40.x86_64 127/152 Installing : elfutils-debuginfod-client-0.190-4.fc40.x86_64 128/152 Installing : binutils-gold-2.41-26.fc40.x86_64 129/152 Running scriptlet: binutils-gold-2.41-26.fc40.x86_64 129/152 Installing : binutils-2.41-26.fc40.x86_64 130/152 Running scriptlet: binutils-2.41-26.fc40.x86_64 130/152 Installing : elfutils-0.190-4.fc40.x86_64 131/152 Installing : gdb-minimal-14.1-4.fc40.x86_64 132/152 Installing : debugedit-5.0-12.fc40.x86_64 133/152 Installing : curl-8.5.0-1.fc40.x86_64 134/152 Installing : rpm-sequoia-1.5.0-2.fc40.x86_64 135/152 Installing : rpm-libs-4.19.1-2.fc40.x86_64 136/152 Running scriptlet: rpm-4.19.1-2.fc40.x86_64 137/152 Installing : rpm-4.19.1-2.fc40.x86_64 137/152 Installing : efi-srpm-macros-5-9.fc39.noarch 138/152 Installing : lua-srpm-macros-1-9.fc39.noarch 139/152 Installing : zig-srpm-macros-1-1.fc40.noarch 140/152 Installing : rpm-build-libs-4.19.1-2.fc40.x86_64 141/152 Installing : ansible-srpm-macros-1-12.fc40.noarch 142/152 Installing : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 143/152 Installing : forge-srpm-macros-0.2.0-1.fc40.noarch 144/152 Installing : go-srpm-macros-3.3.1-1.fc40.noarch 145/152 Installing : python-srpm-macros-3.12-5.fc40.noarch 146/152 Installing : redhat-rpm-config-280-1.fc40.noarch 147/152 Installing : rpm-build-4.19.1-2.fc40.x86_64 148/152 Installing : pyproject-srpm-macros-1.11.0-1.fc40.noarch 149/152 Installing : util-linux-2.39.3-2.fc40.x86_64 150/152 Installing : which-2.21-40.fc39.x86_64 151/152 Installing : info-7.1-1.fc40.x86_64 152/152 Running scriptlet: filesystem-3.18-6.fc39.x86_64 152/152 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 152/152 Running scriptlet: authselect-libs-1.5.0-1.fc40.x86_64 152/152 Running scriptlet: rpm-4.19.1-2.fc40.x86_64 152/152 Running scriptlet: info-7.1-1.fc40.x86_64 152/152 Installed: alternatives-1.26-1.fc40.x86_64 ansible-srpm-macros-1-12.fc40.noarch audit-libs-4.0-1.fc40.x86_64 authselect-1.5.0-1.fc40.x86_64 authselect-libs-1.5.0-1.fc40.x86_64 basesystem-11-18.fc39.noarch bash-5.2.21-2.fc40.x86_64 binutils-2.41-26.fc40.x86_64 binutils-gold-2.41-26.fc40.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch coreutils-9.4-3.fc40.x86_64 coreutils-common-9.4-3.fc40.x86_64 cpio-2.14-5.fc40.x86_64 cracklib-2.9.11-2.fc39.x86_64 crypto-policies-20231204-1.git1e3a2e4.fc40.noarch curl-8.5.0-1.fc40.x86_64 cyrus-sasl-lib-2.1.28-17.fc40.x86_64 debugedit-5.0-12.fc40.x86_64 diffutils-3.10-3.fc39.x86_64 dwz-0.15-3.fc39.x86_64 ed-1.19-4.fc39.x86_64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-4.fc40.x86_64 elfutils-debuginfod-client-0.190-4.fc40.x86_64 elfutils-default-yama-scope-0.190-4.fc40.noarch elfutils-libelf-0.190-4.fc40.x86_64 elfutils-libs-0.190-4.fc40.x86_64 fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.29.noarch fedora-release-common-40-0.29.noarch fedora-release-identity-basic-40-0.29.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-1.fc40.x86_64 file-libs-5.45-1.fc40.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-1:4.9.0-6.fc40.x86_64 fonts-srpm-macros-1:2.0.5-12.fc39.noarch forge-srpm-macros-0.2.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.3.0-1.fc40.x86_64 gdb-minimal-14.1-4.fc40.x86_64 gdbm-1:1.23-4.fc39.x86_64 gdbm-libs-1:1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-3.fc40.noarch glibc-2.38.9000-33.fc40.x86_64 glibc-common-2.38.9000-33.fc40.x86_64 glibc-gconv-extra-2.38.9000-33.fc40.x86_64 glibc-minimal-langpack-2.38.9000-33.fc40.x86_64 gmp-1:6.2.1-5.fc39.x86_64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc40.noarch grep-3.11-5.fc40.x86_64 gzip-1.12-6.fc39.x86_64 info-7.1-1.fc40.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.3-1.fc40.x86_64 krb5-libs-1.21.2-3.fc40.x86_64 libacl-2.3.1-11.fc40.x86_64 libarchive-3.7.2-1.fc40.x86_64 libattr-2.5.2-1.fc40.x86_64 libblkid-2.39.3-2.fc40.x86_64 libbrotli-1.1.0-1.fc40.x86_64 libcap-2.69-1.fc40.x86_64 libcap-ng-0.8.4-2.fc40.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.5.0-1.fc40.x86_64 libeconf-0.5.2-1.fc40.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.3-2.fc40.x86_64 libffi-3.4.4-5.fc40.x86_64 libgcc-14.0.1-0.1.fc40.x86_64 libgomp-14.0.1-0.1.fc40.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.3-2.fc40.x86_64 libnghttp2-1.58.0-1.fc40.x86_64 libnsl2-2.0.0-6.fc39.x86_64 libpkgconf-1.9.5-2.fc39.x86_64 libpsl-0.21.5-1.fc40.x86_64 libpwquality-1.4.5-6.fc39.x86_64 libselinux-3.6-2.fc40.x86_64 libsemanage-3.6-1.fc40.x86_64 libsepol-3.6-1.fc40.x86_64 libsmartcols-2.39.3-2.fc40.x86_64 libssh-0.10.6-2.fc40.x86_64 libssh-config-0.10.6-2.fc40.noarch libstdc++-14.0.1-0.1.fc40.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-1.rc1.fc40.x86_64 libunistring-1.1-5.fc40.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.3-2.fc40.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-4.fc40.x86_64 libxml2-2.12.4-1.fc40.x86_64 libzstd-1.5.5-4.fc39.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.1-1.fc40.x86_64 ncurses-base-6.4-9.20240113.fc40.noarch ncurses-libs-6.4-9.20240113.fc40.x86_64 ocaml-srpm-macros-9-1.fc40.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.x86_64 openssl-libs-1:3.1.4-1.fc40.x86_64 p11-kit-0.25.3-1.fc40.x86_64 p11-kit-trust-0.25.3-1.fc40.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-9.fc40.x86_64 pam-libs-1.5.3-9.fc40.x86_64 patch-2.7.6-22.fc39.x86_64 pcre2-10.42-2.fc40.x86_64 pcre2-syntax-10.42-2.fc40.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.x86_64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.x86_64 popt-1.19-3.fc39.x86_64 publicsuffix-list-dafsa-20240107-1.fc40.noarch pyproject-srpm-macros-1.11.0-1.fc40.noarch python-srpm-macros-3.12-5.fc40.noarch qt5-srpm-macros-5.15.12-1.fc40.noarch qt6-srpm-macros-6.6.1-3.fc40.noarch readline-8.2-4.fc39.x86_64 redhat-rpm-config-280-1.fc40.noarch rpm-4.19.1-2.fc40.x86_64 rpm-build-4.19.1-2.fc40.x86_64 rpm-build-libs-4.19.1-2.fc40.x86_64 rpm-libs-4.19.1-2.fc40.x86_64 rpm-sequoia-1.5.0-2.fc40.x86_64 rust-srpm-macros-25.2-2.fc40.noarch sed-4.8-14.fc39.x86_64 setup-2.14.5-1.fc40.noarch shadow-utils-2:4.14.0-2.fc40.x86_64 sqlite-libs-3.45.0-1.fc40.x86_64 systemd-libs-255.2-2.fc40.x86_64 tar-2:1.35-2.fc40.x86_64 unzip-6.0-62.fc39.x86_64 util-linux-2.39.3-2.fc40.x86_64 util-linux-core-2.39.3-2.fc40.x86_64 which-2.21-40.fc39.x86_64 xxhash-libs-0.8.2-1.fc39.x86_64 xz-5.4.5-1.fc40.x86_64 xz-libs-5.4.5-1.fc40.x86_64 zig-srpm-macros-1-1.fc40.noarch zip-3.0-39.fc40.x86_64 zlib-ng-compat-2.1.6-1.fc40.x86_64 zstd-1.5.5-4.fc39.x86_64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.26-1.fc40.x86_64 ansible-srpm-macros-1-12.fc40.noarch audit-libs-4.0-1.fc40.x86_64 authselect-1.5.0-1.fc40.x86_64 authselect-libs-1.5.0-1.fc40.x86_64 basesystem-11-18.fc39.noarch bash-5.2.21-2.fc40.x86_64 binutils-2.41-26.fc40.x86_64 binutils-gold-2.41-26.fc40.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch coreutils-9.4-3.fc40.x86_64 coreutils-common-9.4-3.fc40.x86_64 cpio-2.14-5.fc40.x86_64 cracklib-2.9.11-2.fc39.x86_64 crypto-policies-20231204-1.git1e3a2e4.fc40.noarch curl-8.5.0-1.fc40.x86_64 cyrus-sasl-lib-2.1.28-17.fc40.x86_64 debugedit-5.0-12.fc40.x86_64 diffutils-3.10-3.fc39.x86_64 dwz-0.15-3.fc39.x86_64 ed-1.19-4.fc39.x86_64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-4.fc40.x86_64 elfutils-debuginfod-client-0.190-4.fc40.x86_64 elfutils-default-yama-scope-0.190-4.fc40.noarch elfutils-libelf-0.190-4.fc40.x86_64 elfutils-libs-0.190-4.fc40.x86_64 fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.29.noarch fedora-release-common-40-0.29.noarch fedora-release-identity-basic-40-0.29.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-1.fc40.x86_64 file-libs-5.45-1.fc40.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-4.9.0-6.fc40.x86_64 fonts-srpm-macros-2.0.5-12.fc39.noarch forge-srpm-macros-0.2.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.3.0-1.fc40.x86_64 gdb-minimal-14.1-4.fc40.x86_64 gdbm-1.23-4.fc39.x86_64 gdbm-libs-1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-3.fc40.noarch glibc-2.38.9000-33.fc40.x86_64 glibc-common-2.38.9000-33.fc40.x86_64 glibc-gconv-extra-2.38.9000-33.fc40.x86_64 glibc-minimal-langpack-2.38.9000-33.fc40.x86_64 gmp-6.2.1-5.fc39.x86_64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc40.noarch grep-3.11-5.fc40.x86_64 gzip-1.12-6.fc39.x86_64 info-7.1-1.fc40.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.3-1.fc40.x86_64 krb5-libs-1.21.2-3.fc40.x86_64 libacl-2.3.1-11.fc40.x86_64 libarchive-3.7.2-1.fc40.x86_64 libattr-2.5.2-1.fc40.x86_64 libblkid-2.39.3-2.fc40.x86_64 libbrotli-1.1.0-1.fc40.x86_64 libcap-2.69-1.fc40.x86_64 libcap-ng-0.8.4-2.fc40.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.5.0-1.fc40.x86_64 libeconf-0.5.2-1.fc40.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.3-2.fc40.x86_64 libffi-3.4.4-5.fc40.x86_64 libgcc-14.0.1-0.1.fc40.x86_64 libgomp-14.0.1-0.1.fc40.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.3-2.fc40.x86_64 libnghttp2-1.58.0-1.fc40.x86_64 libnsl2-2.0.0-6.fc39.x86_64 libpkgconf-1.9.5-2.fc39.x86_64 libpsl-0.21.5-1.fc40.x86_64 libpwquality-1.4.5-6.fc39.x86_64 libselinux-3.6-2.fc40.x86_64 libsemanage-3.6-1.fc40.x86_64 libsepol-3.6-1.fc40.x86_64 libsmartcols-2.39.3-2.fc40.x86_64 libssh-0.10.6-2.fc40.x86_64 libssh-config-0.10.6-2.fc40.noarch libstdc++-14.0.1-0.1.fc40.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-1.rc1.fc40.x86_64 libunistring-1.1-5.fc40.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.3-2.fc40.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-4.fc40.x86_64 libxml2-2.12.4-1.fc40.x86_64 libzstd-1.5.5-4.fc39.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.1-1.fc40.x86_64 ncurses-base-6.4-9.20240113.fc40.noarch ncurses-libs-6.4-9.20240113.fc40.x86_64 ocaml-srpm-macros-9-1.fc40.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.x86_64 openssl-libs-3.1.4-1.fc40.x86_64 p11-kit-0.25.3-1.fc40.x86_64 p11-kit-trust-0.25.3-1.fc40.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-9.fc40.x86_64 pam-libs-1.5.3-9.fc40.x86_64 patch-2.7.6-22.fc39.x86_64 pcre2-10.42-2.fc40.x86_64 pcre2-syntax-10.42-2.fc40.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.x86_64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.x86_64 popt-1.19-3.fc39.x86_64 publicsuffix-list-dafsa-20240107-1.fc40.noarch pyproject-srpm-macros-1.11.0-1.fc40.noarch python-srpm-macros-3.12-5.fc40.noarch qt5-srpm-macros-5.15.12-1.fc40.noarch qt6-srpm-macros-6.6.1-3.fc40.noarch readline-8.2-4.fc39.x86_64 redhat-rpm-config-280-1.fc40.noarch rpm-4.19.1-2.fc40.x86_64 rpm-build-4.19.1-2.fc40.x86_64 rpm-build-libs-4.19.1-2.fc40.x86_64 rpm-libs-4.19.1-2.fc40.x86_64 rpm-sequoia-1.5.0-2.fc40.x86_64 rust-srpm-macros-25.2-2.fc40.noarch sed-4.8-14.fc39.x86_64 setup-2.14.5-1.fc40.noarch shadow-utils-4.14.0-2.fc40.x86_64 sqlite-libs-3.45.0-1.fc40.x86_64 systemd-libs-255.2-2.fc40.x86_64 tar-1.35-2.fc40.x86_64 unzip-6.0-62.fc39.x86_64 util-linux-2.39.3-2.fc40.x86_64 util-linux-core-2.39.3-2.fc40.x86_64 which-2.21-40.fc39.x86_64 xxhash-libs-0.8.2-1.fc39.x86_64 xz-5.4.5-1.fc40.x86_64 xz-libs-5.4.5-1.fc40.x86_64 zig-srpm-macros-1-1.fc40.noarch zip-3.0-39.fc40.x86_64 zlib-ng-compat-2.1.6-1.fc40.x86_64 zstd-1.5.5-4.fc39.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1705622400 Wrote: /builddir/build/SRPMS/snakemake-8.1.2-2.fc40.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-x86_64-1705640458.173212/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-x86_64-1705640458.173212/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-x86_64-1705640458.173212/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-8xe39ldh/snakemake/snakemake.spec) Config(child) 2 minutes 15 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/snakemake-8.1.2-2.fc40.src.rpm) Config(fedora-39-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1705640458.173212/root. INFO: reusing tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1705640458.173212/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1705640458.173212/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-4.19.0-1.fc39.x86_64 rpm-sequoia-1.5.0-1.fc39.x86_64 python3-dnf-4.18.2-1.fc40.noarch python3-dnf-plugins-core-4.4.4-1.fc40.noarch yum-4.18.2-1.fc40.noarch Finish: chroot init Start: build phase for snakemake-8.1.2-2.fc40.src.rpm Start: build setup for snakemake-8.1.2-2.fc40.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1705622400 Wrote: /builddir/build/SRPMS/snakemake-8.1.2-2.fc40.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 38 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 6.6 kB/s | 3.8 kB 00:00 fedora 829 kB/s | 24 kB 00:00 updates 753 kB/s | 23 kB 00:00 Dependencies resolved. ==================================================================================================================================================================== Package Arch Version Repository Size ==================================================================================================================================================================== Installing: help2man noarch 1.49.3-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 217 k latexmk noarch 4.82a-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 425 k librsvg2-tools x86_64 2.57.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.8 M make x86_64 1:4.4.1-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 581 k python3-boto3 noarch 1.34.22-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 339 k python3-devel x86_64 3.12.1-2.fc40 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==================================================================================================================================================================== Install 703 Packages Total download size: 383 M Installed size: 1.2 G Downloading Packages: (1/703): libsvm-3.32-2.fc39.x86_64.rpm 5.2 MB/s | 332 kB 00:00 (2/703): graphite2-1.3.14-13.fc40.x86_64.rpm 1.2 MB/s | 96 kB 00:00 (3/703): python3-pandas-1.5.3-7.fc39~bootstrap. 39 MB/s | 7.1 MB 00:00 (4/703): abattis-cantarell-vf-fonts-0.301-10.fc 703 kB/s | 121 kB 00:00 (5/703): adobe-mappings-cmap-deprecated-2023062 2.9 MB/s | 113 kB 00:00 (6/703): abseil-cpp-20230802.1-2.fc40.x86_64.rp 2.8 MB/s | 663 kB 00:00 (7/703): adobe-mappings-pdf-20190401-5.fc39.noa 11 MB/s | 689 kB 00:00 (8/703): atk-2.50.1-1.fc40.x86_64.rpm 1.6 MB/s | 79 kB 00:00 (9/703): at-spi2-core-2.50.1-1.fc40.x86_64.rpm 4.2 MB/s | 349 kB 00:00 (10/703): adobe-mappings-cmap-20230622-1.fc39.n 9.6 MB/s | 2.1 MB 00:00 (11/703): avahi-libs-0.8-24.fc39.x86_64.rpm 1.5 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ghostscript-tools-printing-10.02.1-5.fc40.x86_64 681/703 Installing : ghostscript-10.02.1-5.fc40.x86_64 682/703 Installing : texlive-dvisvgm-11:svn66532-77.fc39.x86_64 683/703 Installing : abseil-cpp-20230802.1-2.fc40.x86_64 684/703 Installing : python3-grpcio-1.48.4-31.fc40.x86_64 685/703 Installing : python3-grpcio-status-1.48.4-31.fc40.noarch 686/703 Installing : python3-google-api-core-1:2.11.1-5.fc39.noarch 687/703 Installing : python3-google-cloud-core-2.3.3-2.fc39.noarch 688/703 Installing : libsvm-3.32-2.fc39.x86_64 689/703 Installing : clisp-2.49.93-35.20230718git6692497.fc40.x86_64 690/703 Installing : texlive-xindy-11:svn65958-77.fc39.x86_64 691/703 Installing : python3-google-cloud-storage-2.14.0-2.fc40.noarc 692/703 Installing : python3-sphinx-latex-1:7.2.6-4.fc40.noarch 693/703 Installing : latexmk-4.82a-1.fc40.noarch 694/703 Installing : librsvg2-tools-2.57.1-1.fc40.x86_64 695/703 Installing : make-1:4.4.1-2.fc39.x86_64 696/703 Installing : help2man-1.49.3-3.fc39.noarch 697/703 Installing : python3-snakemake-storage-plugin-s3-0.2.8-1.fc40 698/703 Installing : python3-pandas-1.5.3-7.fc39~bootstrap.x86_64 699/703 Installing : python3-pytest-7.4.3-1.fc40.noarch 700/703 Installing : python3-flask-1:3.0.0-1.fc40.noarch 701/703 Installing : python3-snakemake-executor-plugin-cluster-generi 702/703 Installing : python3-devel-3.12.1-2.fc40.x86_64 703/703 Running scriptlet: texlive-base-11:20230311-77.fc39.x86_64 703/703 Running scriptlet: urw-base35-bookman-fonts-20200910-18.fc39.noarch 703/703 Running scriptlet: urw-base35-c059-fonts-20200910-18.fc39.noarch 703/703 Running scriptlet: urw-base35-d050000l-fonts-20200910-18.fc39.noarc 703/703 Running scriptlet: urw-base35-gothic-fonts-20200910-18.fc39.noarch 703/703 Running scriptlet: urw-base35-nimbus-mono-ps-fonts-20200910-18.fc39 703/703 Running scriptlet: urw-base35-nimbus-roman-fonts-20200910-18.fc39.n 703/703 Running scriptlet: urw-base35-nimbus-sans-fonts-20200910-18.fc39.no 703/703 Running scriptlet: urw-base35-p052-fonts-20200910-18.fc39.noarch 703/703 Running scriptlet: urw-base35-standard-symbols-ps-fonts-20200910-18 703/703 Running scriptlet: urw-base35-z003-fonts-20200910-18.fc39.noarch 703/703 Running scriptlet: fontconfig-2.15.0-1.fc40.x86_64 703/703 Running scriptlet: python3-devel-3.12.1-2.fc40.x86_64 703/703 Installed: abattis-cantarell-vf-fonts-0.301-10.fc39.noarch abseil-cpp-20230802.1-2.fc40.x86_64 adobe-mappings-cmap-20230622-1.fc39.noarch adobe-mappings-cmap-deprecated-20230622-1.fc39.noarch adobe-mappings-pdf-20190401-5.fc39.noarch at-spi2-core-2.50.1-1.fc40.x86_64 atk-2.50.1-1.fc40.x86_64 avahi-libs-0.8-24.fc39.x86_64 biber-2.19-3.fc39.noarch c-ares-1.25.0-1.fc40.x86_64 cairo-1.18.0-1.fc40.x86_64 cairo-gobject-1.18.0-1.fc40.x86_64 clisp-2.49.93-35.20230718git6692497.fc40.x86_64 cups-libs-1:2.4.7-7.fc40.x86_64 dbus-1:1.14.10-1.fc40.x86_64 dbus-broker-35-2.fc40.x86_64 dbus-common-1:1.14.10-1.fc40.noarch dbus-libs-1:1.14.10-1.fc40.x86_64 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groff-base-1.23.0-4.fc40.x86_64 grpc-data-1.48.4-31.fc40.noarch gtk-update-icon-cache-3.24.39-1.fc40.x86_64 gtk2-2.24.33-15.fc39.x86_64 guile22-2.2.7-9.fc39.x86_64 gumbo-parser-1:0.10.1-29.fc39.x86_64 harfbuzz-8.3.0-2.fc40.x86_64 help2man-1.49.3-3.fc39.noarch hicolor-icon-theme-0.17-16.fc39.noarch highway-1.0.7-1.fc40.x86_64 hwdata-0.378-1.fc40.noarch jbig2dec-libs-0.20-1.fc40.x86_64 jbigkit-libs-2.1-27.fc40.x86_64 latexmk-4.82a-1.fc40.noarch lcms2-2.15-2.fc39.x86_64 leptonica-1.84.1-1.fc40.x86_64 libICE-1.1.1-1.fc40.x86_64 libSM-1.2.4-1.fc40.x86_64 libX11-1.8.7-1.fc40.x86_64 libX11-common-1.8.7-1.fc40.noarch libX11-xcb-1.8.7-1.fc40.x86_64 libXau-1.0.11-4.fc40.x86_64 libXaw-1.0.15-1.fc40.x86_64 libXcomposite-0.4.6-1.fc40.x86_64 libXcursor-1.2.1-5.fc40.x86_64 libXdamage-1.1.6-1.fc40.x86_64 libXext-1.3.5-4.fc40.x86_64 libXfixes-6.0.1-1.fc40.x86_64 libXft-2.3.8-4.fc40.x86_64 libXi-1.8.1-3.fc40.x86_64 libXinerama-1.1.5-4.fc40.x86_64 libXmu-1.1.4-4.fc40.x86_64 libXpm-3.5.17-1.fc40.x86_64 libXrandr-1.5.4-1.fc40.x86_64 libXrender-0.9.11-4.fc40.x86_64 libXt-1.3.0-1.fc40.x86_64 libXtst-1.2.4-4.fc40.x86_64 libXxf86vm-1.1.5-4.fc40.x86_64 libaom-3.8.0-1.fc40.x86_64 libavif-0.11.1-12.fc40.x86_64 libb2-0.98.1-9.fc39.x86_64 libdatrie-0.2.13-7.fc39.x86_64 libdav1d-1.3.0-1.fc40.x86_64 libdb-5.3.28-59.fc40.x86_64 libdrm-2.4.120-1.fc40.x86_64 libgfortran-14.0.1-0.1.fc40.x86_64 libglade2-2.6.4-30.fc39.x86_64 libglvnd-1:1.7.0-1.fc40.x86_64 libglvnd-glx-1:1.7.0-1.fc40.x86_64 libgs-10.02.1-5.fc40.x86_64 libicu-73.2-3.fc40.x86_64 libijs-0.35-20.fc40.x86_64 libimagequant-4.0.3-2.fc40.x86_64 libjpeg-turbo-2.1.4-3.fc39.x86_64 libjxl-1:0.8.2-3.fc40.x86_64 liblerc-4.0.0-4.fc39.x86_64 libpaper-1:2.1.1-1.fc39.x86_64 libpciaccess-0.16-9.fc39.x86_64 libpng-2:1.6.40-1.fc40.x86_64 libpq-16.1-1.fc40.x86_64 libquadmath-14.0.1-0.1.fc40.x86_64 librsvg2-2.57.1-1.fc40.x86_64 librsvg2-tools-2.57.1-1.fc40.x86_64 libsigsegv-2.14-5.fc39.x86_64 libsvm-3.32-2.fc39.x86_64 libthai-0.1.29-6.fc39.x86_64 libtiff-4.5.0-3.fc40.x86_64 libtool-ltdl-2.4.7-9.fc40.x86_64 libvmaf-2.3.0-6.fc39.x86_64 libwebp-1.3.2-2.fc40.x86_64 libxcb-1.16-2.fc40.x86_64 libxshmfence-1.3.2-1.fc40.x86_64 libxslt-1.1.39-1.fc40.x86_64 mailcap-2.1.54-2.fc39.noarch make-1:4.4.1-2.fc39.x86_64 mesa-libGL-23.3.3-1.fc40.x86_64 mesa-libglapi-23.3.3-1.fc40.x86_64 mpdecimal-2.5.1-7.fc39.x86_64 mupdf-1.23.7-3.fc40.x86_64 ncurses-6.4-9.20240113.fc40.x86_64 nettle-3.9.1-2.fc39.x86_64 openblas-0.3.26-1.fc40.x86_64 openblas-openmp-0.3.26-1.fc40.x86_64 openjpeg2-2.5.0-5.fc40.x86_64 pango-1.51.0-1.fc40.x86_64 pari-2.15.4-2.fc39.x86_64 perl-Authen-SASL-2.1700-1.fc40.noarch perl-AutoLoader-5.74-504.fc40.noarch perl-B-1.88-504.fc40.x86_64 perl-B-Hooks-EndOfScope-0.26-7.fc39.noarch perl-Business-ISBN-3.008-2.fc39.noarch perl-Business-ISBN-Data-20240116.001-1.fc40.noarch perl-Business-ISMN-1.203-2.fc39.noarch perl-Business-ISSN-1.005-8.fc39.noarch perl-Carp-1.54-500.fc39.noarch perl-Class-Accessor-0.51-18.fc39.noarch perl-Class-Data-Inheritable-0.09-6.fc39.noarch perl-Class-Inspector-1.36-14.fc39.noarch perl-Class-Method-Modifiers-2.15-2.fc39.noarch perl-Class-Singleton-1.6-9.fc39.noarch perl-Class-Struct-0.68-504.fc40.noarch perl-Clone-0.46-4.fc39.x86_64 perl-Compress-Raw-Bzip2-2.206-1.fc39.x86_64 perl-Compress-Raw-Zlib-2.206-2.fc40.x86_64 perl-Convert-ASN1-0.34-1.fc40.noarch perl-Data-Compare-1.29-2.fc39.noarch perl-Data-Dump-1.25-8.fc39.noarch perl-Data-Dumper-2.188-501.fc39.x86_64 perl-Data-OptList-0.114-2.fc39.noarch perl-Data-Uniqid-0.12-31.fc39.noarch perl-Date-ISO8601-0.005-18.fc39.noarch perl-Date-Manip-6.94-1.fc40.noarch perl-DateTime-2:1.65-1.fc40.x86_64 perl-DateTime-Calendar-Julian-0.107-5.fc39.noarch perl-DateTime-Format-Builder-0.8300-11.fc39.noarch perl-DateTime-Format-Strptime-1:1.79-8.fc39.noarch perl-DateTime-Locale-1.40-1.fc40.noarch perl-DateTime-TimeZone-2.61-1.fc40.noarch perl-DateTime-TimeZone-SystemV-0.010-19.fc39.noarch perl-DateTime-TimeZone-Tzfile-0.011-19.fc39.noarch perl-Devel-CallChecker-0.009-3.fc39.x86_64 perl-Devel-Caller-2.07-3.fc39.x86_64 perl-Devel-GlobalDestruction-0.14-22.fc39.noarch perl-Devel-LexAlias-0.05-34.fc39.x86_64 perl-Devel-StackTrace-1:2.05-1.fc40.noarch perl-Digest-1.20-500.fc39.noarch perl-Digest-HMAC-1.04-8.fc39.noarch perl-Digest-MD5-2.59-1.fc40.x86_64 perl-Digest-SHA-1:6.04-501.fc39.x86_64 perl-Dist-CheckConflicts-0.11-28.fc39.noarch perl-DynaLoader-1.54-504.fc40.x86_64 perl-DynaLoader-Functions-0.004-2.fc39.noarch perl-Email-Date-Format-1.008-2.fc39.noarch perl-Encode-4:3.20-501.fc40.x86_64 perl-Encode-Locale-1.05-27.fc39.noarch perl-English-1.11-504.fc40.noarch perl-Env-1.06-500.fc39.noarch perl-Errno-1.37-504.fc40.x86_64 perl-Eval-Closure-0.14-21.fc39.noarch perl-Exception-Class-1.45-8.fc39.noarch perl-Exporter-5.78-1.fc40.noarch perl-ExtUtils-MM-Utils-2:7.70-501.fc39.noarch perl-Fcntl-1.15-504.fc40.x86_64 perl-File-Basename-2.86-504.fc40.noarch perl-File-Compare-1.100.700-504.fc40.noarch perl-File-Copy-2.41-504.fc40.noarch perl-File-Find-1.43-504.fc40.noarch perl-File-Find-Rule-0.34-26.fc39.noarch perl-File-Listing-6.16-1.fc39.noarch perl-File-Path-2.18-501.fc40.noarch perl-File-ShareDir-1.118-9.fc39.noarch perl-File-Slurper-0.014-3.fc39.noarch perl-File-Temp-1:0.231.100-501.fc40.noarch perl-File-stat-1.13-504.fc40.noarch perl-FileHandle-2.05-504.fc40.noarch perl-Filter-2:1.64-501.fc39.x86_64 perl-GSSAPI-0.28-43.fc39.x86_64 perl-Getopt-Long-1:2.57-1.fc40.noarch perl-Getopt-Std-1.13-504.fc40.noarch perl-HTML-Parser-3.81-3.fc39.x86_64 perl-HTML-Tagset-3.20-55.fc40.noarch perl-HTTP-Cookies-6.11-1.fc40.noarch perl-HTTP-Date-6.06-2.fc39.noarch perl-HTTP-Message-6.45-1.fc40.noarch perl-HTTP-Negotiate-6.01-36.fc39.noarch perl-HTTP-Tiny-0.088-3.fc39.noarch perl-Hash-Util-FieldHash-1.26-504.fc40.x86_64 perl-I18N-LangTags-0.45-504.fc40.noarch perl-I18N-Langinfo-0.22-504.fc40.x86_64 perl-IO-1.52-504.fc40.x86_64 perl-IO-Compress-2.206-1.fc39.noarch perl-IO-HTML-1.004-11.fc39.noarch perl-IO-Socket-IP-0.42-1.fc39.noarch perl-IO-Socket-SSL-2.084-1.fc40.noarch perl-IO-String-1.08-48.fc39.noarch perl-IPC-Cmd-2:1.04-502.fc40.noarch perl-IPC-Open3-1.22-504.fc40.noarch perl-IPC-Run3-0.048-29.fc39.noarch perl-IPC-SysV-2.09-503.fc40.x86_64 perl-IPC-System-Simple-1.30-11.fc39.noarch perl-JSON-4.10-3.fc39.noarch perl-LDAP-1:0.68-11.fc39.noarch perl-LWP-MediaTypes-6.04-15.fc39.noarch perl-LWP-Protocol-https-6.11-1.fc39.noarch perl-Lingua-Translit-0.29-4.fc39.noarch perl-List-AllUtils-0.19-10.fc39.noarch perl-List-SomeUtils-0.59-3.fc39.noarch perl-List-UtilsBy-0.12-7.fc39.noarch perl-Locale-Maketext-1.33-501.fc39.noarch perl-Locale-Maketext-Simple-1:0.21-504.fc40.noarch perl-Log-Dispatch-2.71-2.fc39.noarch perl-Log-Dispatch-FileRotate-1.38-7.fc39.noarch perl-Log-Log4perl-1.57-3.fc39.noarch perl-MIME-Base64-3.16-501.fc40.x86_64 perl-MIME-Charset-1.013.1-3.fc39.noarch perl-MIME-Lite-3.033-8.fc39.noarch perl-MIME-Types-2.24-3.fc39.noarch perl-MRO-Compat-0.15-7.fc39.noarch perl-Mail-Sender-1:0.903-22.fc39.noarch perl-Mail-Sendmail-0.80-18.fc39.noarch perl-MailTools-2.21-14.fc39.noarch perl-Math-BigInt-1:2.0030.02-1.fc40.noarch perl-Math-Complex-1.62-504.fc40.noarch perl-Module-CoreList-1:5.20231230-1.fc40.noarch perl-Module-Implementation-0.09-37.fc39.noarch perl-Module-Load-1:0.36-501.fc40.noarch perl-Module-Load-Conditional-0.74-501.fc40.noarch perl-Module-Metadata-1.000038-3.fc39.noarch perl-Module-Runtime-0.016-20.fc39.noarch perl-Mozilla-CA-20231213-1.fc40.noarch perl-NTLM-1.09-36.fc39.noarch perl-Net-HTTP-6.23-2.fc39.noarch perl-Net-SMTP-SSL-1.04-22.fc40.noarch perl-Net-SSLeay-1.94-1.fc40.x86_64 perl-Number-Compare-0.03-36.fc39.noarch perl-Opcode-1.64-504.fc40.x86_64 perl-POSIX-2.13-504.fc40.x86_64 perl-Package-Generator-1.106-29.fc39.noarch perl-Package-Stash-0.40-5.fc39.noarch perl-Package-Stash-XS-0.30-5.fc39.x86_64 perl-PadWalker-2.5-10.fc39.x86_64 perl-Params-Check-1:0.38-500.fc39.noarch perl-Params-Classify-0.015-20.fc39.x86_64 perl-Params-Util-1.102-12.fc39.x86_64 perl-Params-Validate-1.31-5.fc39.x86_64 perl-Params-ValidationCompiler-0.31-3.fc39.noarch perl-Parse-RecDescent-1.967015-20.fc39.noarch perl-PathTools-3.89-500.fc39.x86_64 perl-Pod-Escapes-1:1.07-501.fc40.noarch perl-Pod-Html-1.34-504.fc40.noarch perl-Pod-Perldoc-3.28.01-501.fc39.noarch perl-Pod-Simple-1:3.45-4.fc39.noarch perl-Pod-Usage-4:2.03-500.fc39.noarch perl-Ref-Util-0.204-18.fc39.noarch perl-Ref-Util-XS-0.117-20.fc39.x86_64 perl-Regexp-Common-2017060201-22.fc39.noarch perl-Role-Tiny-2.002004-9.fc39.noarch perl-Safe-2.44-504.fc40.noarch perl-Scalar-List-Utils-5:1.63-500.fc39.x86_64 perl-SelectSaver-1.02-504.fc40.noarch perl-Socket-4:2.037-3.fc39.x86_64 perl-Sort-Key-1.33-28.fc39.x86_64 perl-Specio-0.48-4.fc39.noarch perl-Storable-1:3.32-500.fc39.x86_64 perl-Sub-Exporter-0.991-1.fc40.noarch perl-Sub-Exporter-Progressive-0.001013-22.fc39.noarch perl-Sub-Identify-0.14-24.fc39.x86_64 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urw-base35-bookman-fonts-20200910-18.fc39.noarch urw-base35-c059-fonts-20200910-18.fc39.noarch urw-base35-d050000l-fonts-20200910-18.fc39.noarch urw-base35-fonts-20200910-18.fc39.noarch urw-base35-fonts-common-20200910-18.fc39.noarch urw-base35-gothic-fonts-20200910-18.fc39.noarch urw-base35-nimbus-mono-ps-fonts-20200910-18.fc39.noarch urw-base35-nimbus-roman-fonts-20200910-18.fc39.noarch urw-base35-nimbus-sans-fonts-20200910-18.fc39.noarch urw-base35-p052-fonts-20200910-18.fc39.noarch urw-base35-standard-symbols-ps-fonts-20200910-18.fc39.noarch urw-base35-z003-fonts-20200910-18.fc39.noarch vim-filesystem-2:9.1.031-1.fc40.noarch xdg-utils-1.2.0~git20231511.21fb316-1.fc40.noarch xml-common-0.6.3-62.fc40.noarch xpdf-libs-1:4.04-10.fc39.x86_64 xprop-1.2.5-4.fc39.x86_64 zziplib-0.13.72-5.fc39.x86_64 Complete! Finish: build setup for snakemake-8.1.2-2.fc40.src.rpm Start: rpmbuild snakemake-8.1.2-2.fc40.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1705622400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.QbwctI + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf snakemake-8.1.2 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/snakemake-8.1.2.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd snakemake-8.1.2 + rm -rf /builddir/build/BUILD/snakemake-8.1.2-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/snakemake-8.1.2-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/snakemake-7.11.0-docs-no-animated-demo.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + '[' -z sP ']' + shebang_flags=-kasP + /usr/bin/python3 -B /usr/lib/rpm/redhat/pathfix.py -pni /usr/bin/python3 -kasP . recursedown('.') recursedown('./.github') recursedown('./.github/ISSUE_TEMPLATE') 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recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/one/simulations/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/one/simulations/alpha~2/gamma~3.9') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/plots/alpha_is_1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/plots/alpha_is_1/beta_is_0.1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/plots/alpha_is_2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/plots/alpha_is_2/beta_is_0.0') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations/alpha_is_1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations/alpha_is_1/beta_is_0.1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations/alpha_is_2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep/simulations/alpha_is_2/beta_is_0.0') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep_and_pattern') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep_and_pattern/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/sep_and_pattern/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/plots') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/plots/alpha~1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/plots/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/simulations') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/simulations/alpha~1') recursedown('./tests/test_paramspace_single_wildcard/expected-results/results/two/simulations/alpha~2') recursedown('./tests/test_paramspace_single_wildcard/scripts') recursedown('./tests/test_parser') recursedown('./tests/test_parser/expected-results') recursedown('./tests/test_parsing_terminal_comment_following_statement') recursedown('./tests/test_parsing_terminal_comment_following_statement/expected-results') recursedown('./tests/test_pathlib') recursedown('./tests/test_pathlib/expected-results') recursedown('./tests/test_pathlib/expected-results/outdir') recursedown('./tests/test_pathlib/expected-results/outdir/function_unpacking') recursedown('./tests/test_pathlib_missing_file') recursedown('./tests/test_pathlib_missing_file/expected-results') recursedown('./tests/test_pep_pathlib') recursedown('./tests/test_pep_pathlib/expected-results') recursedown('./tests/test_pep_pathlib/pep') recursedown('./tests/test_pep_pathlib/workflow') recursedown('./tests/test_pep_pathlib/workflow/schemas') recursedown('./tests/test_peppy') recursedown('./tests/test_peppy/expected-results') recursedown('./tests/test_peppy/pep') recursedown('./tests/test_peppy/workflow') recursedown('./tests/test_peppy/workflow/schemas') recursedown('./tests/test_persistent_dict') recursedown('./tests/test_persistent_dict/expected-results') recursedown('./tests/test_pipe_depend') recursedown('./tests/test_pipe_depend/expected-results') recursedown('./tests/test_pipes') recursedown('./tests/test_pipes/expected-results') recursedown('./tests/test_pipes2') recursedown('./tests/test_pipes2/expected-results') recursedown('./tests/test_pipes_fail') recursedown('./tests/test_pipes_fail/expected-results') recursedown('./tests/test_pipes_multiple') recursedown('./tests/test_pipes_multiple/expected-results') recursedown('./tests/test_prebuilt_conda_script') recursedown('./tests/test_prebuilt_conda_script/dummy_package') recursedown('./tests/test_prebuilt_conda_script/dummy_package/src') recursedown('./tests/test_prebuilt_conda_script/dummy_package/src/dummy') recursedown('./tests/test_prebuilt_conda_script/dummy_package/src/dummy.egg-info') recursedown('./tests/test_prebuilt_conda_script/expected-results') recursedown('./tests/test_profile') recursedown('./tests/test_profile/expected-results') recursedown('./tests/test_protected_symlink_output') recursedown('./tests/test_protected_symlink_output/expected-results') recursedown('./tests/test_r_wrapper') recursedown('./tests/test_remote_auto') recursedown('./tests/test_remote_auto/expected-results') recursedown('./tests/test_remote_azure') recursedown('./tests/test_remote_gs') recursedown('./tests/test_remote_gs/expected-results') recursedown('./tests/test_remote_irods') recursedown('./tests/test_remote_irods/expected-results') recursedown('./tests/test_remote_irods/setup-data') recursedown('./tests/test_remote_irods/test-data') recursedown('./tests/test_remote_log') recursedown('./tests/test_remote_log/expected-results') recursedown('./tests/test_remote_ncbi') recursedown('./tests/test_remote_ncbi/expected-results') recursedown('./tests/test_remote_ncbi_simple') recursedown('./tests/test_remote_ncbi_simple/expected-results') recursedown('./tests/test_remote_sftp') recursedown('./tests/test_remote_sftp/expected-results') recursedown('./tests/test_remote_zenodo') recursedown('./tests/test_remote_zenodo/expected-results') recursedown('./tests/test_report') recursedown('./tests/test_report/.snakemake') recursedown('./tests/test_report/.snakemake/metadata') recursedown('./tests/test_report/data') recursedown('./tests/test_report/envs') recursedown('./tests/test_report/expected-results') recursedown('./tests/test_report/report') recursedown('./tests/test_report/testdir') recursedown('./tests/test_report_dir') recursedown('./tests/test_report_dir/expected-results') recursedown('./tests/test_report_dir/test') recursedown('./tests/test_report_dir/test/js') recursedown('./tests/test_report_display_code') recursedown('./tests/test_report_display_code/expected-results') recursedown('./tests/test_report_zip') recursedown('./tests/test_report_zip/.snakemake') recursedown('./tests/test_report_zip/.snakemake/metadata') recursedown('./tests/test_report_zip/data') recursedown('./tests/test_report_zip/envs') ./setup.py: no change ./versioneer.py: no change ./.github/workflows/scripts/sacct-proxy.py: updating ./apidocs/conf.py: updating ./docs/conf.py: updating ./examples/hello-world/scripts/plot-hist.py: no change ./snakemake/__init__.py: no change ./snakemake/__main__.py: no change ./snakemake/_version.py: no change ./snakemake/api.py: no change ./snakemake/benchmark.py: no change ./snakemake/checkpoints.py: no change ./snakemake/cli.py: no change ./snakemake/cwl.py: no change ./snakemake/dag.py: no change ./snakemake/decorators.py: no change ./snakemake/exceptions.py: no change ./snakemake/gui.py: no change ./snakemake/io.py: no change ./snakemake/jobs.py: no change ./snakemake/logging.py: no change ./snakemake/modules.py: no change ./snakemake/notebook.py: no change ./snakemake/output_index.py: no change ./snakemake/parser.py: no change ./snakemake/path_modifier.py: no change ./snakemake/persistence.py: no change ./snakemake/profiles.py: no change ./snakemake/resources.py: no change ./snakemake/ruleinfo.py: no change ./snakemake/rules.py: no change ./snakemake/scheduler.py: no change ./snakemake/settings.py: no change ./snakemake/shell.py: no change ./snakemake/sourcecache.py: no change ./snakemake/spawn_jobs.py: no change ./snakemake/storage.py: no change ./snakemake/target_jobs.py: no change ./snakemake/utils.py: no change ./snakemake/workflow.py: no change ./snakemake/wrapper.py: no change ./snakemake/caching/__init__.py: no change ./snakemake/caching/hash.py: no change ./snakemake/caching/local.py: no change ./snakemake/caching/storage.py: no change ./snakemake/common/__init__.py: no change ./snakemake/common/argparse.py: no change ./snakemake/common/configfile.py: no change ./snakemake/common/git.py: no change ./snakemake/common/tbdstring.py: no change ./snakemake/common/workdir_handler.py: no change ./snakemake/common/tests/__init__.py: no change ./snakemake/common/tests/testcases/__init__.py: no change ./snakemake/common/tests/testcases/groups/__init__.py: no change ./snakemake/common/tests/testcases/simple/__init__.py: no change ./snakemake/deployment/__init__.py: no change ./snakemake/deployment/conda.py: no change ./snakemake/deployment/containerize.py: no change ./snakemake/deployment/env_modules.py: no change ./snakemake/deployment/singularity.py: no change ./snakemake/executors/__init__.py: no change ./snakemake/executors/dryrun.py: no change ./snakemake/executors/google_lifesciences_helper.py: updating ./snakemake/executors/local.py: no change ./snakemake/executors/touch.py: no change ./snakemake/linting/__init__.py: no change ./snakemake/linting/links.py: no change ./snakemake/linting/rules.py: no change ./snakemake/linting/snakefiles.py: no change ./snakemake/remote/AzBlob.py: no change ./snakemake/remote/EGA.py: no change ./snakemake/remote/FTP.py: no change ./snakemake/remote/GS.py: no change ./snakemake/remote/HTTP.py: no change ./snakemake/remote/NCBI.py: no change ./snakemake/remote/S3.py: no change ./snakemake/remote/S3Mocked.py: no change ./snakemake/remote/SFTP.py: no change ./snakemake/remote/XRootD.py: no change ./snakemake/remote/__init__.py: no change ./snakemake/remote/dropbox.py: no change ./snakemake/remote/gfal.py: no change ./snakemake/remote/gridftp.py: no change ./snakemake/remote/iRODS.py: no change ./snakemake/remote/webdav.py: no change ./snakemake/remote/zenodo.py: no change ./snakemake/report/__init__.py: no change ./snakemake/report/rulegraph_spec.py: no change ./snakemake/report/data/__init__.py: no change ./snakemake/report/data/categories.py: no change ./snakemake/report/data/common.py: no change ./snakemake/report/data/packages.py: no change ./snakemake/report/data/results.py: no change ./snakemake/report/data/rulegraph.py: no change ./snakemake/report/data/rules.py: no change ./snakemake/report/data/runtimes.py: no change ./snakemake/report/data/timeline.py: no change ./snakemake/report/template/__init__.py: no change ./snakemake/report/template/components/__init__.py: no change ./snakemake/script/__init__.py: no change ./snakemake/template_rendering/__init__.py: no change ./snakemake/template_rendering/jinja2.py: no change ./snakemake/template_rendering/yte.py: no change ./snakemake/unit_tests/__init__.py: no change ./snakemake/unit_tests/templates/__init__.py: no change ./tests/__init__.py: no change ./tests/common.py: no change ./tests/conftest.py: no change ./tests/test_api.py: no change ./tests/test_executor_test_suite.py: no change ./tests/test_expand.py: no change ./tests/test_io.py: no change ./tests/test_linting.py: no change ./tests/test_persistence.py: no change ./tests/test_schema.py: no change ./tests/test_script.py: no change ./tests/testapi.py: no change ./tests/tests.py: no change ./tests/test_benchmark/script.py: updating ./tests/test_conda_python_3_7_script/test_script.py: no change ./tests/test_conda_python_script/test_script.py: no change ./tests/test_deploy_sources/scripts/test.py: no change ./tests/test_filegraph/scripts/vis.py: no change ./tests/test_generate_unit_tests/expected-results/.tests/unit/test_a.py: no change ./tests/test_generate_unit_tests/expected-results/.tests/unit/test_all.py: no change ./tests/test_generate_unit_tests/expected-results/.tests/unit/test_b.py: no change ./tests/test_get_log_both/wrapper.py: no change ./tests/test_get_log_complex/wrapper.py: no change ./tests/test_get_log_none/wrapper.py: no change ./tests/test_get_log_stderr/wrapper.py: no change ./tests/test_get_log_stdout/wrapper.py: no change ./tests/test_github_issue1158/qsub.py: updating ./tests/test_github_issue627/job.py: updating ./tests/test_github_issue_14/local_script.py: no change ./tests/test_github_issue_14/pythonTest.py: updating ./tests/test_handover/script.py: no change ./tests/test_issue1046/my_wrapper/wrapper.py: no change ./tests/test_issue916/local_script.py: no change ./tests/test_issue916/pythonTest.py: updating ./tests/test_job_properties/qsub.py: updating ./tests/test_local_import/bar.py: no change ./tests/test_local_import/foo/__init__.py: no change ./tests/test_paramspace/scripts/simulate.py: no change ./tests/test_paramspace_single_wildcard/scripts/simulate.py: no change ./tests/test_pipes/producer.py: no change ./tests/test_prebuilt_conda_script/test.py: no change ./tests/test_prebuilt_conda_script/dummy_package/src/dummy/__init__.py: no change ./tests/test_prebuilt_conda_script/dummy_package/src/dummy/dummy.py: no change ./tests/test_report_display_code/test.py: no change ./tests/test_restartable_job_cmd_exit_1/qsub.py: updating ./tests/test_restartable_job_qsub_exit_1/qsub.py: updating ./tests/test_script/scripts/test.py: no change ./tests/test_script_pre_py39/script.py: no change ./tests/test_script_py/scripts/test.py: no change ./tests/test_singularity/script.py: no change ./tests/test_singularity_module/script.py: no change ./tests/test_string_resources/qsub.py: updating ./tests/test_tibanna/cleanup.py: no change ./tests/test_tibanna/scripts/step2.py: no change 'misc/nano/README.md' -> 'README-nano.md' 'misc/vim/README.md' -> 'README-vim.md' Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.dselph recursedown('./tests/test_report_zip/expected-results') recursedown('./tests/test_report_zip/report') recursedown('./tests/test_report_zip/testdir') recursedown('./tests/test_restartable_job_cmd_exit_1') recursedown('./tests/test_restartable_job_cmd_exit_1/expected-results') recursedown('./tests/test_restartable_job_qsub_exit_1') recursedown('./tests/test_restartable_job_qsub_exit_1/expected-results') recursedown('./tests/test_retries') recursedown('./tests/test_retries/expected-results') recursedown('./tests/test_retries_not_overriden') recursedown('./tests/test_retries_not_overriden/expected-results') recursedown('./tests/test_rule_defined_in_for_loop') recursedown('./tests/test_rule_defined_in_for_loop/expected-results') recursedown('./tests/test_rule_inheritance_globals') recursedown('./tests/test_rule_inheritance_globals/.snakemake') recursedown('./tests/test_rule_inheritance_globals/.snakemake/metadata') recursedown('./tests/test_rule_inheritance_globals/expected-results') recursedown('./tests/test_ruledag') recursedown('./tests/test_ruledeps') recursedown('./tests/test_ruledeps/expected-results') recursedown('./tests/test_run_namedlist') recursedown('./tests/test_run_namedlist/expected-results') recursedown('./tests/test_same_wildcard') recursedown('./tests/test_same_wildcard/expected-results') recursedown('./tests/test_scatter_gather') recursedown('./tests/test_scatter_gather/expected-results') recursedown('./tests/test_scatter_gather/expected-results/gathered') recursedown('./tests/test_scatter_gather/expected-results/splitted') recursedown('./tests/test_scatter_gather_multiple_processes') recursedown('./tests/test_scatter_gather_multiple_processes/expected-results') recursedown('./tests/test_scatter_gather_multiple_processes/expected-results/gathered') recursedown('./tests/test_scatter_gather_multiple_processes/expected-results/split_a') recursedown('./tests/test_scatter_gather_multiple_processes/expected-results/split_b') recursedown('./tests/test_script') recursedown('./tests/test_script/envs') recursedown('./tests/test_script/expected-results') recursedown('./tests/test_script/scripts') recursedown('./tests/test_script_pre_py39') recursedown('./tests/test_script_pre_py39/expected-results') recursedown('./tests/test_script_py') recursedown('./tests/test_script_py/expected-results') recursedown('./tests/test_script_py/scripts') recursedown('./tests/test_service_jobs') recursedown('./tests/test_service_jobs/expected-results') recursedown('./tests/test_set_resources') recursedown('./tests/test_set_resources/expected-results') recursedown('./tests/test_shadow') recursedown('./tests/test_shadow/expected-results') recursedown('./tests/test_shadow_copy') recursedown('./tests/test_shadow_copy/expected-results') recursedown('./tests/test_shadow_prefix') recursedown('./tests/test_shadow_prefix/expected-results') recursedown('./tests/test_shadowed_log') recursedown('./tests/test_shadowed_log/expected-results') recursedown('./tests/test_shell') recursedown('./tests/test_shell/expected-results') recursedown('./tests/test_singularity') recursedown('./tests/test_singularity/expected-results') recursedown('./tests/test_singularity_conda') recursedown('./tests/test_singularity_conda/expected-results') recursedown('./tests/test_singularity_global') recursedown('./tests/test_singularity_global/expected-results') recursedown('./tests/test_singularity_module') recursedown('./tests/test_singularity_module/expected-results') recursedown('./tests/test_singularity_none') recursedown('./tests/test_singularity_none/expected-results') recursedown('./tests/test_slurm_mpi') recursedown('./tests/test_slurm_mpi/envs') recursedown('./tests/test_slurm_mpi/expected-results') recursedown('./tests/test_solver') recursedown('./tests/test_solver/expected-results') recursedown('./tests/test_source_path') recursedown('./tests/test_source_path/expected-results') recursedown('./tests/test_source_path/workflow') recursedown('./tests/test_source_path/workflow/resources') recursedown('./tests/test_spaces_in_fnames') recursedown('./tests/test_spaces_in_fnames/expected-results') recursedown('./tests/test_speed') recursedown('./tests/test_storage') recursedown('./tests/test_storage/expected-results') recursedown('./tests/test_strict_mode') recursedown('./tests/test_strict_mode/expected-results') recursedown('./tests/test_string_resources') recursedown('./tests/test_string_resources/expected-results') recursedown('./tests/test_subworkflow_config') recursedown('./tests/test_subworkflow_config/expected-results') recursedown('./tests/test_subworkflows') recursedown('./tests/test_subworkflows/expected-results') recursedown('./tests/test_symlink_temp') recursedown('./tests/test_symlink_temp/expected-results') recursedown('./tests/test_symlink_time_handling') recursedown('./tests/test_symlink_time_handling/expected-results') recursedown('./tests/test_temp') recursedown('./tests/test_temp/expected-results') recursedown('./tests/test_temp_expand') recursedown('./tests/test_temp_expand/expected-results') recursedown('./tests/test_template_engine') recursedown('./tests/test_template_engine/expected-results') recursedown('./tests/test_tes') recursedown('./tests/test_tes/expected-results') recursedown('./tests/test_threads') recursedown('./tests/test_threads/expected-results') recursedown('./tests/test_threads0') recursedown('./tests/test_threads0/expected-results') recursedown('./tests/test_tibanna') recursedown('./tests/test_tibanna/expected-results') recursedown('./tests/test_tibanna/scripts') recursedown('./tests/test_tmpdir') recursedown('./tests/test_tmpdir/expected-results') recursedown('./tests/test_touch') recursedown('./tests/test_touch/expected-results') recursedown('./tests/test_touch_pipeline_with_temp_dir') recursedown('./tests/test_touch_pipeline_with_temp_dir/expected-results') recursedown('./tests/test_touch_remote_prefix') recursedown('./tests/test_touch_remote_prefix/expected-results') recursedown('./tests/test_touch_with_directories') recursedown('./tests/test_touch_with_directories/expected-results') recursedown('./tests/test_unpack_dict') recursedown('./tests/test_unpack_dict/expected-results') recursedown('./tests/test_unpack_list') recursedown('./tests/test_unpack_list/expected-results') recursedown('./tests/test_until') recursedown('./tests/test_until/expected-results') recursedown('./tests/test_update_config') recursedown('./tests/test_update_config/expected-results') recursedown('./tests/test_url_include') recursedown('./tests/test_url_include/expected-results') recursedown('./tests/test_use_rule_same_module') recursedown('./tests/test_use_rule_same_module/expected-results') recursedown('./tests/test_validate') recursedown('./tests/test_validate/expected-results') recursedown('./tests/test_wildcard_count_ambiguity') recursedown('./tests/test_wildcard_count_ambiguity/expected-results') recursedown('./tests/test_wildcard_keyword') recursedown('./tests/test_wildcard_keyword/expected-results') recursedown('./tests/test_workflow_profile') recursedown('./tests/test_workflow_profile/dummy-general-profile') recursedown('./tests/test_workflow_profile/expected-results') recursedown('./tests/test_workflow_profile/workflow') recursedown('./tests/test_workflow_profile/workflow/profiles') recursedown('./tests/test_workflow_profile/workflow/profiles/default') recursedown('./tests/test_wrapper') recursedown('./tests/test_wrapper/expected-results') recursedown('./tests/test_xrootd') recursedown('./tests/test_yaml_config') recursedown('./tests/test_yaml_config/expected-results') + sed -r -i '1{/^#!/d}' snakemake/executors/jobscript.sh snakemake/executors/google_lifesciences_helper.py + sed -r -i 's@"python"@"/usr/bin/python3"@g' tests/test_linting.py + sed -r -i 's@python -m@"/usr/bin/python3 -m@g' tests/tests.py + sed -r -i 's/^(sphinxcontrib-napoleon|lutra)/# &/' docs/requirements.txt + echo 'latex_engine = '\''xelatex'\''' + for editor in nano vim + cp -vp misc/nano/README.md README-nano.md + for editor in nano vim + cp -vp misc/vim/README.md README-vim.md + RPM_EC=0 ++ jobs -p + exit 0 + umask 022 + cd /builddir/build/BUILD + cd snakemake-8.1.2 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + TMPDIR=/builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir + RPM_TOXENV=py312 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/snakemake-8.1.2/pyproject-wheeldir --output /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-buildrequires -x reports,messaging,google-cloud,azure docs/requirements.txt Handling sphinx >=3 from requirements file docs/requirements.txt Requirement satisfied: sphinx >=3 (installed: sphinx 7.2.6) Handling sphinx-argparse from requirements file docs/requirements.txt Requirement not satisfied: sphinx-argparse Handling docutils from requirements file docs/requirements.txt Requirement satisfied: docutils (installed: docutils 0.20.1) Handling myst-parser from requirements file docs/requirements.txt Requirement not satisfied: myst-parser Handling configargparse from requirements file docs/requirements.txt Requirement satisfied: configargparse (installed: configargparse 1.7) Handling appdirs from requirements file docs/requirements.txt Requirement not satisfied: appdirs Handling snakemake-interface-common from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-common (installed: snakemake-interface-common 1.15.1) Handling snakemake-interface-executor-plugins from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-executor-plugins (installed: snakemake-interface-executor-plugins 8.1.3) Handling snakemake-interface-storage-plugins from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-storage-plugins (installed: snakemake-interface-storage-plugins 3.0.0) Exiting dependency generation pass: all requirements files + cat /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/snakemake-8.1.2-2.fc40.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 45 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 4.8 kB/s | 3.8 kB 00:00 fedora 333 kB/s | 24 kB 00:00 updates 718 kB/s | 23 kB 00:00 Package librsvg2-tools-2.57.1-1.fc40.x86_64 is already installed. Package texlive-xindy-11:svn65958-77.fc39.x86_64 is already installed. Package help2man-1.49.3-3.fc39.noarch is already installed. Package latexmk-4.82a-1.fc40.noarch is already installed. Package make-1:4.4.1-2.fc39.x86_64 is already installed. Package pyproject-rpm-macros-1.11.0-1.fc40.noarch is already installed. Package python3-devel-3.12.1-2.fc40.x86_64 is already installed. Package python3-devel-3.12.1-2.fc40.x86_64 is already installed. Package python3-sphinx-latex-1:7.2.6-4.fc40.noarch is already installed. Package python3-boto3-1.34.22-1.fc40.noarch is already installed. Package python3-configargparse-1.7-1.fc40.noarch is already installed. Package python3-docutils-0.20.1-1.fc40.noarch is already installed. Package python3-flask-1:3.0.0-1.fc40.noarch is already installed. Package python3-google-cloud-storage-2.14.0-2.fc40.noarch is already installed. Package python3-packaging-23.2-2.fc40.noarch is already installed. Package python3-pandas-1.5.3-7.fc39~bootstrap.x86_64 is already installed. Package python3-pytest-7.4.3-1.fc40.noarch is already installed. Package python3-snakemake-executor-plugin-cluster-generic-1.0.7-1.fc40.noarch is already installed. Package python3-snakemake-interface-common-1.15.1-1.fc40.noarch is already installed. Package python3-snakemake-interface-executor-plugins-8.1.3-2.fc40~bootstrap.noarch is already installed. Package python3-snakemake-interface-storage-plugins-3.0.0-2.fc40~bootstrap.noarch is already installed. Package python3-snakemake-storage-plugin-s3-0.2.8-1.fc40.noarch is already installed. Package python3-sphinx-1:7.2.6-4.fc40.noarch is already installed. Package texlive-xetex-11:svn66203-77.fc39.x86_64 is already installed. Package vim-filesystem-2:9.1.031-1.fc40.noarch is already installed. Dependencies resolved. ===================================================================================================================== Package Arch Version Repository Size ===================================================================================================================== Installing: python3-appdirs noarch 1.4.4-11.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 23 k python3-myst-parser noarch 2.0.0-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 185 k python3-pip noarch 23.3.1-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 2.9 M python3-sphinx-argparse noarch 0.4.0-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 39 k Installing dependencies: libyaml x86_64 0.2.5-12.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 59 k python3-markdown-it-py noarch 3.0.0-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 165 k python3-mdit-py-plugins noarch 0.4.0-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 101 k python3-mdurl noarch 0.1.2-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 26 k python3-pyyaml x86_64 6.0.1-11.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 218 k Transaction Summary ===================================================================================================================== Install 9 Packages Total download size: 3.7 M Installed size: 17 M Downloading Packages: (1/9): python3-appdirs-1.4.4-11.fc39.noarch.rpm 28 kB/s | 23 kB 00:00 (2/9): libyaml-0.2.5-12.fc39.x86_64.rpm 68 kB/s | 59 kB 00:00 (3/9): python3-markdown-it-py-3.0.0-2.fc39.noar 185 kB/s | 165 kB 00:00 (4/9): python3-mdurl-0.1.2-4.fc39.noarch.rpm 588 kB/s | 26 kB 00:00 (5/9): python3-mdit-py-plugins-0.4.0-2.fc39.noa 938 kB/s | 101 kB 00:00 (6/9): python3-myst-parser-2.0.0-3.fc40.noarch. 2.1 MB/s | 185 kB 00:00 (7/9): python3-pyyaml-6.0.1-11.fc39.x86_64.rpm 2.5 MB/s | 218 kB 00:00 (8/9): python3-sphinx-argparse-0.4.0-4.fc39.noa 689 kB/s | 39 kB 00:00 (9/9): python3-pip-23.3.1-3.fc40.noarch.rpm 14 MB/s | 2.9 MB 00:00 -------------------------------------------------------------------------------- Total 3.3 MB/s | 3.7 MB 00:01 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-mdurl-0.1.2-4.fc39.noarch 1/9 Installing : python3-markdown-it-py-3.0.0-2.fc39.noarch 2/9 Installing : python3-mdit-py-plugins-0.4.0-2.fc39.noarch 3/9 Installing : libyaml-0.2.5-12.fc39.x86_64 4/9 Installing : python3-pyyaml-6.0.1-11.fc39.x86_64 5/9 Installing : python3-myst-parser-2.0.0-3.fc40.noarch 6/9 Installing : python3-sphinx-argparse-0.4.0-4.fc39.noarch 7/9 Installing : python3-pip-23.3.1-3.fc40.noarch 8/9 Installing : python3-appdirs-1.4.4-11.fc39.noarch 9/9 Running scriptlet: python3-appdirs-1.4.4-11.fc39.noarch 9/9 Installed: libyaml-0.2.5-12.fc39.x86_64 python3-appdirs-1.4.4-11.fc39.noarch python3-markdown-it-py-3.0.0-2.fc39.noarch python3-mdit-py-plugins-0.4.0-2.fc39.noarch python3-mdurl-0.1.2-4.fc39.noarch python3-myst-parser-2.0.0-3.fc40.noarch python3-pip-23.3.1-3.fc40.noarch python3-pyyaml-6.0.1-11.fc39.x86_64 python3-sphinx-argparse-0.4.0-4.fc39.noarch Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1705622400 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.AVkFLY + umask 022 + cd /builddir/build/BUILD + cd snakemake-8.1.2 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + TMPDIR=/builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir + RPM_TOXENV=py312 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/snakemake-8.1.2/pyproject-wheeldir --output /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-buildrequires -x reports,messaging,google-cloud,azure docs/requirements.txt Handling sphinx >=3 from requirements file docs/requirements.txt Requirement satisfied: sphinx >=3 (installed: sphinx 7.2.6) Handling sphinx-argparse from requirements file docs/requirements.txt Requirement satisfied: sphinx-argparse (installed: sphinx-argparse 0.4.0) Handling docutils from requirements file docs/requirements.txt Requirement satisfied: docutils (installed: docutils 0.20.1) Handling myst-parser from requirements file docs/requirements.txt Requirement satisfied: myst-parser (installed: myst-parser 2.0.0) Handling configargparse from requirements file docs/requirements.txt Requirement satisfied: configargparse (installed: configargparse 1.7) Handling appdirs from requirements file docs/requirements.txt Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling snakemake-interface-common from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-common (installed: snakemake-interface-common 1.15.1) Handling snakemake-interface-executor-plugins from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-executor-plugins (installed: snakemake-interface-executor-plugins 8.1.3) Handling snakemake-interface-storage-plugins from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-storage-plugins (installed: snakemake-interface-storage-plugins 3.0.0) Handling setuptools>=42 from build-system.requires Requirement satisfied: setuptools>=42 (installed: setuptools 68.2.2) Handling tomli; python_version < "3.11" from build-system.requires Ignoring alien requirement: tomli; python_version < "3.11" running egg_info creating snakemake.egg-info writing snakemake.egg-info/PKG-INFO writing dependency_links to snakemake.egg-info/dependency_links.txt writing entry points to snakemake.egg-info/entry_points.txt writing requirements to snakemake.egg-info/requires.txt writing top-level names to snakemake.egg-info/top_level.txt writing manifest file 'snakemake.egg-info/SOURCES.txt' reading manifest file 'snakemake.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.md' writing manifest file 'snakemake.egg-info/SOURCES.txt' Handling wheel from get_requires_for_build_wheel Requirement not satisfied: wheel Exiting dependency generation pass: get_requires_for_build_wheel + cat /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-buildrequires + rm -rfv '*.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/snakemake-8.1.2-2.fc40.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 43 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 40 kB/s | 3.8 kB 00:00 fedora 592 kB/s | 24 kB 00:00 updates 703 kB/s | 23 kB 00:00 Package librsvg2-tools-2.57.1-1.fc40.x86_64 is already installed. Package texlive-xindy-11:svn65958-77.fc39.x86_64 is already installed. Package help2man-1.49.3-3.fc39.noarch is already installed. Package latexmk-4.82a-1.fc40.noarch is already installed. Package make-1:4.4.1-2.fc39.x86_64 is already installed. Package pyproject-rpm-macros-1.11.0-1.fc40.noarch is already installed. Package python3-devel-3.12.1-2.fc40.x86_64 is already installed. Package python3-devel-3.12.1-2.fc40.x86_64 is already installed. Package python3-sphinx-latex-1:7.2.6-4.fc40.noarch is already installed. Package python3-appdirs-1.4.4-11.fc39.noarch is already installed. Package python3-boto3-1.34.22-1.fc40.noarch is already installed. Package python3-configargparse-1.7-1.fc40.noarch is already installed. Package python3-docutils-0.20.1-1.fc40.noarch is already installed. Package python3-flask-1:3.0.0-1.fc40.noarch is already installed. Package python3-google-cloud-storage-2.14.0-2.fc40.noarch is already installed. Package python3-myst-parser-2.0.0-3.fc40.noarch is already installed. Package python3-packaging-23.2-2.fc40.noarch is already installed. Package python3-pandas-1.5.3-7.fc39~bootstrap.x86_64 is already installed. Package python3-pip-23.3.1-3.fc40.noarch is already installed. Package python3-pytest-7.4.3-1.fc40.noarch is already installed. Package python3-setuptools-68.2.2-1.fc40.noarch is already installed. Package python3-snakemake-executor-plugin-cluster-generic-1.0.7-1.fc40.noarch is already installed. Package python3-snakemake-interface-common-1.15.1-1.fc40.noarch is already installed. Package python3-snakemake-interface-executor-plugins-8.1.3-2.fc40~bootstrap.noarch is already installed. Package python3-snakemake-interface-storage-plugins-3.0.0-2.fc40~bootstrap.noarch is already installed. Package python3-snakemake-storage-plugin-s3-0.2.8-1.fc40.noarch is already installed. Package python3-sphinx-1:7.2.6-4.fc40.noarch is already installed. Package python3-sphinx-argparse-0.4.0-4.fc39.noarch is already installed. Package texlive-xetex-11:svn66203-77.fc39.x86_64 is already installed. Package vim-filesystem-2:9.1.031-1.fc40.noarch is already installed. Dependencies resolved. ============================================================================================================= Package Arch Version Repository Size ============================================================================================================= Installing: python3-wheel noarch 1:0.41.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 148 k Transaction Summary ============================================================================================================= Install 1 Package Total download size: 148 k Installed size: 507 k Downloading Packages: python3-wheel-0.41.2-1.fc40.noarch.rpm 964 kB/s | 148 kB 00:00 -------------------------------------------------------------------------------- Total 953 kB/s | 148 kB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-wheel-1:0.41.2-1.fc40.noarch 1/1 Running scriptlet: python3-wheel-1:0.41.2-1.fc40.noarch 1/1 Installed: python3-wheel-1:0.41.2-1.fc40.noarch Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1705622400 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.DYQpO9 + umask 022 + cd /builddir/build/BUILD + cd snakemake-8.1.2 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + TMPDIR=/builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir + RPM_TOXENV=py312 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/snakemake-8.1.2/pyproject-wheeldir --output /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-buildrequires -x reports,messaging,google-cloud,azure docs/requirements.txt Handling sphinx >=3 from requirements file docs/requirements.txt Requirement satisfied: sphinx >=3 (installed: sphinx 7.2.6) Handling sphinx-argparse from requirements file docs/requirements.txt Requirement satisfied: sphinx-argparse (installed: sphinx-argparse 0.4.0) Handling docutils from requirements file docs/requirements.txt Requirement satisfied: docutils (installed: docutils 0.20.1) Handling myst-parser from requirements file docs/requirements.txt Requirement satisfied: myst-parser (installed: myst-parser 2.0.0) Handling configargparse from requirements file docs/requirements.txt Requirement satisfied: configargparse (installed: configargparse 1.7) Handling appdirs from requirements file docs/requirements.txt Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling snakemake-interface-common from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-common (installed: snakemake-interface-common 1.15.1) Handling snakemake-interface-executor-plugins from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-executor-plugins (installed: snakemake-interface-executor-plugins 8.1.3) Handling snakemake-interface-storage-plugins from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-storage-plugins (installed: snakemake-interface-storage-plugins 3.0.0) Handling setuptools>=42 from build-system.requires Requirement satisfied: setuptools>=42 (installed: setuptools 68.2.2) Handling tomli; python_version < "3.11" from build-system.requires Ignoring alien requirement: tomli; python_version < "3.11" running egg_info writing snakemake.egg-info/PKG-INFO writing dependency_links to snakemake.egg-info/dependency_links.txt writing entry points to snakemake.egg-info/entry_points.txt writing requirements to snakemake.egg-info/requires.txt writing top-level names to snakemake.egg-info/top_level.txt reading manifest file 'snakemake.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.md' writing manifest file 'snakemake.egg-info/SOURCES.txt' Handling wheel from get_requires_for_build_wheel Requirement satisfied: wheel (installed: wheel 0.41.2) running dist_info writing snakemake.egg-info/PKG-INFO writing dependency_links to snakemake.egg-info/dependency_links.txt writing entry points to snakemake.egg-info/entry_points.txt writing requirements to snakemake.egg-info/requires.txt writing top-level names to snakemake.egg-info/top_level.txt reading manifest file 'snakemake.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.md' writing manifest file 'snakemake.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/snakemake-8.1.2/snakemake-8.1.2.dist-info' Handling appdirs from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling immutables from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: immutables Handling configargparse from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: configargparse (installed: configargparse 1.7) Handling connection-pool >=0.0.3 from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: connection-pool >=0.0.3 Handling datrie from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: datrie Handling docutils from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: docutils (installed: docutils 0.20.1) Handling gitpython from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: gitpython Handling humanfriendly from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: humanfriendly Handling jinja2 <4.0,>=3.0 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: jinja2 <4.0,>=3.0 (installed: jinja2 3.1.3) Handling jsonschema from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: jsonschema Handling nbformat from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: nbformat Handling packaging from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: packaging (installed: packaging 23.2) Handling psutil from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: psutil Handling pulp <2.9,>=2.3.1 from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: pulp <2.9,>=2.3.1 Handling pyyaml from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: pyyaml (installed: pyyaml 6.0.1) Handling requests from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: requests (installed: requests 2.31.0) Handling reretry from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: reretry (installed: reretry 0.11.8) Handling smart-open >=3.0 from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: smart-open >=3.0 Handling snakemake-interface-executor-plugins <9.0,>=8.1.3 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: snakemake-interface-executor-plugins <9.0,>=8.1.3 (installed: snakemake-interface-executor-plugins 8.1.3) Handling snakemake-interface-common <2.0,>=1.15.0 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: snakemake-interface-common <2.0,>=1.15.0 (installed: snakemake-interface-common 1.15.1) Handling snakemake-interface-storage-plugins <4.0,>=3.0.0 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: snakemake-interface-storage-plugins <4.0,>=3.0.0 (installed: snakemake-interface-storage-plugins 3.0.0) Handling stopit from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: stopit Handling tabulate from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: tabulate Handling throttler from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: throttler (installed: throttler 1.2.2) Handling toposort >=1.10 from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: toposort >=1.10 Handling wrapt from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: wrapt (installed: wrapt 1.16.0) Handling yte <2.0,>=1.5.1 from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: yte <2.0,>=1.5.1 Handling conda-inject <2.0,>=1.3.1 from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: conda-inject <2.0,>=1.3.1 Handling slack-sdk ; extra == 'messaging' from hook generated metadata: Requires-Dist (snakemake) Requirement not satisfied: slack-sdk ; extra == 'messaging' Handling eido ; extra == 'pep' from hook generated metadata: Requires-Dist (snakemake) Ignoring alien requirement: eido ; extra == 'pep' Handling peppy ; extra == 'pep' from hook generated metadata: Requires-Dist (snakemake) Ignoring alien requirement: peppy ; extra == 'pep' Handling pygments ; extra == 'reports' from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: pygments ; extra == 'reports' (installed: pygments 2.17.2) + cat /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-buildrequires + rm -rfv snakemake-8.1.2.dist-info/ removed 'snakemake-8.1.2.dist-info/LICENSE.md' removed 'snakemake-8.1.2.dist-info/METADATA' removed 'snakemake-8.1.2.dist-info/entry_points.txt' removed 'snakemake-8.1.2.dist-info/top_level.txt' removed directory 'snakemake-8.1.2.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/snakemake-8.1.2-2.fc40.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 45 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 31 kB/s | 3.8 kB 00:00 fedora 794 kB/s | 24 kB 00:00 updates 698 kB/s | 23 kB 00:00 Package python3-jinja2-3.1.3-1.fc40.noarch is already installed. Package python3-snakemake-interface-common-1.15.1-1.fc40.noarch is already installed. Package python3-snakemake-interface-executor-plugins-8.1.3-2.fc40~bootstrap.noarch is already installed. Package python3-snakemake-interface-storage-plugins-3.0.0-2.fc40~bootstrap.noarch is already installed. Package librsvg2-tools-2.57.1-1.fc40.x86_64 is already installed. Package texlive-xindy-11:svn65958-77.fc39.x86_64 is already installed. Package help2man-1.49.3-3.fc39.noarch is already installed. Package latexmk-4.82a-1.fc40.noarch is already installed. Package make-1:4.4.1-2.fc39.x86_64 is already installed. Package pyproject-rpm-macros-1.11.0-1.fc40.noarch is already installed. Package python3-devel-3.12.1-2.fc40.x86_64 is already installed. Package python3-devel-3.12.1-2.fc40.x86_64 is already installed. Package python3-sphinx-latex-1:7.2.6-4.fc40.noarch is already installed. Package python3-appdirs-1.4.4-11.fc39.noarch is already installed. Package python3-boto3-1.34.22-1.fc40.noarch is already installed. Package python3-configargparse-1.7-1.fc40.noarch is already installed. Package python3-docutils-0.20.1-1.fc40.noarch is already installed. Package python3-flask-1:3.0.0-1.fc40.noarch is already installed. Package python3-google-cloud-storage-2.14.0-2.fc40.noarch is already installed. Package python3-myst-parser-2.0.0-3.fc40.noarch is already installed. Package python3-packaging-23.2-2.fc40.noarch is already installed. Package python3-pandas-1.5.3-7.fc39~bootstrap.x86_64 is already installed. Package python3-pip-23.3.1-3.fc40.noarch is already installed. Package python3-pygments-2.17.2-1.fc40.noarch is already installed. Package python3-pytest-7.4.3-1.fc40.noarch is already installed. Package python3-pyyaml-6.0.1-11.fc39.x86_64 is already installed. Package python3-requests-2.31.0-1.fc40.noarch is already installed. Package python3-reretry-0.11.8-6.fc40.noarch is already installed. Package python3-setuptools-68.2.2-1.fc40.noarch is already installed. Package python3-snakemake-executor-plugin-cluster-generic-1.0.7-1.fc40.noarch is already installed. Package python3-snakemake-interface-common-1.15.1-1.fc40.noarch is already installed. Package python3-snakemake-interface-executor-plugins-8.1.3-2.fc40~bootstrap.noarch is already installed. Package python3-snakemake-interface-storage-plugins-3.0.0-2.fc40~bootstrap.noarch is already installed. Package python3-snakemake-storage-plugin-s3-0.2.8-1.fc40.noarch is already installed. Package python3-sphinx-1:7.2.6-4.fc40.noarch is already installed. Package python3-sphinx-argparse-0.4.0-4.fc39.noarch is already installed. Package python3-throttler-1.2.2-7.fc40.noarch is already installed. Package python3-wheel-1:0.41.2-1.fc40.noarch is already installed. Package python3-wrapt-1.16.0-1.fc40.x86_64 is already installed. Package texlive-xetex-11:svn66203-77.fc39.x86_64 is already installed. Package vim-filesystem-2:9.1.031-1.fc40.noarch is already installed. Dependencies resolved. ========================================================================================================================================= Package Arch Version Repository Size ========================================================================================================================================= Installing: python3-GitPython noarch 3.1.40-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 361 k python3-conda-inject noarch 1.3.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 18 k python3-connection_pool noarch 0.0.3-9.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 17 k python3-datrie x86_64 0.8.2-22.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 157 k python3-humanfriendly noarch 10.0-8.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 131 k python3-immutables x86_64 0.20-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 59 k python3-jsonschema noarch 4.19.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 186 k python3-nbformat noarch 5.9.1-2.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 120 k python3-psutil x86_64 5.9.5-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 258 k python3-pulp noarch 2.7.0-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 195 k python3-slackclient noarch 3.26.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 482 k python3-smart_open noarch 6.4.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 107 k python3-stopit noarch 1.1.2-8.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 25 k python3-tabulate noarch 0.9.0-4.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 69 k python3-toposort noarch 1.10-8.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 20 k python3-yte noarch 1.5.4-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 31 k Installing dependencies: git-core x86_64 2.43.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 4.5 M less x86_64 643-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 176 k libcbor x86_64 0.10.2-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 33 k libedit x86_64 3.1-48.20230828cvs.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 107 k libfido2 x86_64 1.14.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 97 k openssh x86_64 9.6p1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 418 k openssh-clients x86_64 9.6p1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 742 k python3-attrs noarch 23.2.0-2.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 111 k python3-boto noarch 2.49.0-19.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 1.6 M python3-dpath noarch 2.1.4-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 37 k python3-fastjsonschema noarch 2.18.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 56 k python3-gitdb noarch 4.0.10-3.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 128 k python3-jsonschema-specifications noarch 2023.11.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 21 k python3-jupyter-core noarch 5.1.0-5.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 125 k python3-plac noarch 1.4.2-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 61 k python3-platformdirs noarch 3.11.0-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 40 k python3-referencing noarch 0.31.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 73 k python3-rpds-py x86_64 0.16.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 291 k python3-smmap noarch 5.0.0-6.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 55 k python3-traitlets noarch 5.11.2-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 191 k python3-zombie-imp noarch 0.0.2-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 29 k Transaction Summary ========================================================================================================================================= Install 37 Packages Total download size: 11 M Installed size: 51 M Downloading Packages: (1/37): libcbor-0.10.2-3.fc40.x86_64.rpm 214 kB/s | 33 kB 00:00 (2/37): less-643-1.fc40.x86_64.rpm 940 kB/s | 176 kB 00:00 (3/37): libedit-3.1-48.20230828cvs.fc40.x86_64. 1.7 MB/s | 107 kB 00:00 (4/37): libfido2-1.14.0-1.fc40.x86_64.rpm 2.3 MB/s | 97 kB 00:00 (5/37): git-core-2.43.0-1.fc40.x86_64.rpm 13 MB/s | 4.5 MB 00:00 (6/37): openssh-9.6p1-1.fc40.x86_64.rpm 3.3 MB/s | 418 kB 00:00 (7/37): openssh-clients-9.6p1-1.fc40.x86_64.rpm 5.1 MB/s | 742 kB 00:00 (8/37): python3-GitPython-3.1.40-1.fc40.noarch. 6.4 MB/s | 361 kB 00:00 (9/37): python3-attrs-23.2.0-2.fc40.noarch.rpm 2.0 MB/s | 111 kB 00:00 (10/37): python3-conda-inject-1.3.1-1.fc40.noar 286 kB/s | 18 kB 00:00 (11/37): python3-connection_pool-0.0.3-9.fc39.n 267 kB/s | 17 kB 00:00 (12/37): python3-boto-2.49.0-19.fc40.noarch.rpm 17 MB/s | 1.6 MB 00:00 (13/37): python3-datrie-0.8.2-22.fc40.x86_64.rp 2.7 MB/s | 157 kB 00:00 (14/37): python3-dpath-2.1.4-3.fc39.noarch.rpm 664 kB/s | 37 kB 00:00 (15/37): python3-fastjsonschema-2.18.0-1.fc40.n 992 kB/s | 56 kB 00:00 (16/37): python3-gitdb-4.0.10-3.fc39.noarch.rpm 2.1 MB/s | 128 kB 00:00 (17/37): python3-humanfriendly-10.0-8.fc39.noar 2.1 MB/s | 131 kB 00:00 (18/37): python3-immutables-0.20-1.fc40.x86_64. 1.0 MB/s | 59 kB 00:00 (19/37): python3-jsonschema-specifications-2023 402 kB/s | 21 kB 00:00 (20/37): python3-jsonschema-4.19.1-1.fc40.noarc 3.3 MB/s | 186 kB 00:00 (21/37): python3-jupyter-core-5.1.0-5.fc39.noar 2.3 MB/s | 125 kB 00:00 (22/37): python3-plac-1.4.2-3.fc40.noarch.rpm 1.0 MB/s | 61 kB 00:00 (23/37): python3-nbformat-5.9.1-2.fc39.noarch.r 2.0 MB/s | 120 kB 00:00 (24/37): python3-platformdirs-3.11.0-1.fc40.noa 690 kB/s | 40 kB 00:00 (25/37): python3-pulp-2.7.0-3.fc39.noarch.rpm 4.3 MB/s | 195 kB 00:00 (26/37): python3-psutil-5.9.5-2.fc40.x86_64.rpm 5.3 MB/s | 258 kB 00:00 (27/37): python3-referencing-0.31.1-1.fc40.noar 1.5 MB/s | 73 kB 00:00 (28/37): python3-rpds-py-0.16.2-1.fc40.x86_64.r 5.9 MB/s | 291 kB 00:00 (29/37): python3-smart_open-6.4.0-1.fc40.noarch 2.4 MB/s | 107 kB 00:00 (30/37): python3-smmap-5.0.0-6.fc39.noarch.rpm 1.0 MB/s | 55 kB 00:00 (31/37): python3-slackclient-3.26.2-1.fc40.noar 4.7 MB/s | 482 kB 00:00 (32/37): python3-stopit-1.1.2-8.fc39.noarch.rpm 506 kB/s | 25 kB 00:00 (33/37): python3-tabulate-0.9.0-4.fc39.noarch.r 1.6 MB/s | 69 kB 00:00 (34/37): python3-toposort-1.10-8.fc40.noarch.rp 516 kB/s | 20 kB 00:00 (35/37): python3-traitlets-5.11.2-1.fc40.noarch 4.5 MB/s | 191 kB 00:00 (36/37): python3-yte-1.5.4-1.fc40.noarch.rpm 723 kB/s | 31 kB 00:00 (37/37): python3-zombie-imp-0.0.2-3.fc40.noarch 673 kB/s | 29 kB 00:00 -------------------------------------------------------------------------------- Total 12 MB/s | 11 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-traitlets-5.11.2-1.fc40.noarch 1/37 Installing : python3-rpds-py-0.16.2-1.fc40.x86_64 2/37 Installing : python3-attrs-23.2.0-2.fc40.noarch 3/37 Installing : python3-referencing-0.31.1-1.fc40.noarch 4/37 Installing : python3-jsonschema-specifications-2023.11.2-1.fc40 5/37 Installing : python3-jsonschema-4.19.1-1.fc40.noarch 6/37 Installing : python3-zombie-imp-0.0.2-3.fc40.noarch 7/37 Installing : python3-boto-2.49.0-19.fc40.noarch 8/37 Installing : python3-smmap-5.0.0-6.fc39.noarch 9/37 Installing : python3-gitdb-4.0.10-3.fc39.noarch 10/37 Installing : python3-platformdirs-3.11.0-1.fc40.noarch 11/37 Installing : python3-jupyter-core-5.1.0-5.fc39.noarch 12/37 Installing : python3-plac-1.4.2-3.fc40.noarch 13/37 Installing : python3-fastjsonschema-2.18.0-1.fc40.noarch 14/37 Installing : python3-dpath-2.1.4-3.fc39.noarch 15/37 Installing : openssh-9.6p1-1.fc40.x86_64 16/37 Installing : libedit-3.1-48.20230828cvs.fc40.x86_64 17/37 Installing : libcbor-0.10.2-3.fc40.x86_64 18/37 Installing : libfido2-1.14.0-1.fc40.x86_64 19/37 Installing : openssh-clients-9.6p1-1.fc40.x86_64 20/37 Running scriptlet: openssh-clients-9.6p1-1.fc40.x86_64 20/37 Installing : less-643-1.fc40.x86_64 21/37 Installing : git-core-2.43.0-1.fc40.x86_64 22/37 Installing : python3-GitPython-3.1.40-1.fc40.noarch 23/37 Installing : python3-yte-1.5.4-1.fc40.noarch 24/37 Installing : python3-nbformat-5.9.1-2.fc39.noarch 25/37 Installing : python3-smart_open-6.4.0-1.fc40.noarch 26/37 Installing : python3-toposort-1.10-8.fc40.noarch 27/37 Installing : python3-tabulate-0.9.0-4.fc39.noarch 28/37 Installing : python3-stopit-1.1.2-8.fc39.noarch 29/37 Installing : python3-slackclient-3.26.2-1.fc40.noarch 30/37 Installing : python3-pulp-2.7.0-3.fc39.noarch 31/37 Installing : python3-psutil-5.9.5-2.fc40.x86_64 32/37 Installing : python3-immutables-0.20-1.fc40.x86_64 33/37 Installing : python3-humanfriendly-10.0-8.fc39.noarch 34/37 Installing : python3-datrie-0.8.2-22.fc40.x86_64 35/37 Installing : python3-connection_pool-0.0.3-9.fc39.noarch 36/37 Installing : python3-conda-inject-1.3.1-1.fc40.noarch 37/37 Running scriptlet: python3-conda-inject-1.3.1-1.fc40.noarch 37/37 Installed: git-core-2.43.0-1.fc40.x86_64 less-643-1.fc40.x86_64 libcbor-0.10.2-3.fc40.x86_64 libedit-3.1-48.20230828cvs.fc40.x86_64 libfido2-1.14.0-1.fc40.x86_64 openssh-9.6p1-1.fc40.x86_64 openssh-clients-9.6p1-1.fc40.x86_64 python3-GitPython-3.1.40-1.fc40.noarch python3-attrs-23.2.0-2.fc40.noarch python3-boto-2.49.0-19.fc40.noarch python3-conda-inject-1.3.1-1.fc40.noarch python3-connection_pool-0.0.3-9.fc39.noarch python3-datrie-0.8.2-22.fc40.x86_64 python3-dpath-2.1.4-3.fc39.noarch python3-fastjsonschema-2.18.0-1.fc40.noarch python3-gitdb-4.0.10-3.fc39.noarch python3-humanfriendly-10.0-8.fc39.noarch python3-immutables-0.20-1.fc40.x86_64 python3-jsonschema-4.19.1-1.fc40.noarch python3-jsonschema-specifications-2023.11.2-1.fc40.noarch python3-jupyter-core-5.1.0-5.fc39.noarch python3-nbformat-5.9.1-2.fc39.noarch python3-plac-1.4.2-3.fc40.noarch python3-platformdirs-3.11.0-1.fc40.noarch python3-psutil-5.9.5-2.fc40.x86_64 python3-pulp-2.7.0-3.fc39.noarch python3-referencing-0.31.1-1.fc40.noarch python3-rpds-py-0.16.2-1.fc40.x86_64 python3-slackclient-3.26.2-1.fc40.noarch python3-smart_open-6.4.0-1.fc40.noarch python3-smmap-5.0.0-6.fc39.noarch python3-stopit-1.1.2-8.fc39.noarch python3-tabulate-0.9.0-4.fc39.noarch python3-toposort-1.10-8.fc40.noarch python3-traitlets-5.11.2-1.fc40.noarch python3-yte-1.5.4-1.fc40.noarch python3-zombie-imp-0.0.2-3.fc40.noarch Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1705622400 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.jPxRnf + umask 022 + cd /builddir/build/BUILD + cd snakemake-8.1.2 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + TMPDIR=/builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir + RPM_TOXENV=py312 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/snakemake-8.1.2/pyproject-wheeldir --output /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-buildrequires -x reports,messaging,google-cloud,azure docs/requirements.txt Handling sphinx >=3 from requirements file docs/requirements.txt Requirement satisfied: sphinx >=3 (installed: sphinx 7.2.6) Handling sphinx-argparse from requirements file docs/requirements.txt Requirement satisfied: sphinx-argparse (installed: sphinx-argparse 0.4.0) Handling docutils from requirements file docs/requirements.txt Requirement satisfied: docutils (installed: docutils 0.20.1) Handling myst-parser from requirements file docs/requirements.txt Requirement satisfied: myst-parser (installed: myst-parser 2.0.0) Handling configargparse from requirements file docs/requirements.txt Requirement satisfied: configargparse (installed: configargparse 1.7) Handling appdirs from requirements file docs/requirements.txt Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling snakemake-interface-common from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-common (installed: snakemake-interface-common 1.15.1) Handling snakemake-interface-executor-plugins from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-executor-plugins (installed: snakemake-interface-executor-plugins 8.1.3) Handling snakemake-interface-storage-plugins from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-storage-plugins (installed: snakemake-interface-storage-plugins 3.0.0) Handling setuptools>=42 from build-system.requires Requirement satisfied: setuptools>=42 (installed: setuptools 68.2.2) Handling tomli; python_version < "3.11" from build-system.requires Ignoring alien requirement: tomli; python_version < "3.11" running egg_info writing snakemake.egg-info/PKG-INFO writing dependency_links to snakemake.egg-info/dependency_links.txt writing entry points to snakemake.egg-info/entry_points.txt writing requirements to snakemake.egg-info/requires.txt writing top-level names to snakemake.egg-info/top_level.txt reading manifest file 'snakemake.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.md' writing manifest file 'snakemake.egg-info/SOURCES.txt' Handling wheel from get_requires_for_build_wheel Requirement satisfied: wheel (installed: wheel 0.41.2) running dist_info writing snakemake.egg-info/PKG-INFO writing dependency_links to snakemake.egg-info/dependency_links.txt writing entry points to snakemake.egg-info/entry_points.txt writing requirements to snakemake.egg-info/requires.txt writing top-level names to snakemake.egg-info/top_level.txt reading manifest file 'snakemake.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.md' writing manifest file 'snakemake.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/snakemake-8.1.2/snakemake-8.1.2.dist-info' Handling appdirs from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling immutables from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: immutables (installed: immutables 0.20) Handling configargparse from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: configargparse (installed: configargparse 1.7) Handling connection-pool >=0.0.3 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: connection-pool >=0.0.3 (installed: connection-pool 0.0.3) Handling datrie from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: datrie (installed: datrie 0.8.2) Handling docutils from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: docutils (installed: docutils 0.20.1) Handling gitpython from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: gitpython (installed: gitpython 3.1.40) Handling humanfriendly from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: humanfriendly (installed: humanfriendly 10.0) Handling jinja2 <4.0,>=3.0 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: jinja2 <4.0,>=3.0 (installed: jinja2 3.1.3) Handling jsonschema from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: jsonschema (installed: jsonschema 4.19.1) Handling nbformat from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: nbformat (installed: nbformat 5.9.1) Handling packaging from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: packaging (installed: packaging 23.2) Handling psutil from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: psutil (installed: psutil 5.9.5) Handling pulp <2.9,>=2.3.1 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: pulp <2.9,>=2.3.1 (installed: pulp 2.7.0) Handling pyyaml from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: pyyaml (installed: pyyaml 6.0.1) Handling requests from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: requests (installed: requests 2.31.0) Handling reretry from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: reretry (installed: reretry 0.11.8) Handling smart-open >=3.0 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: smart-open >=3.0 (installed: smart-open 6.4.0) Handling snakemake-interface-executor-plugins <9.0,>=8.1.3 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: snakemake-interface-executor-plugins <9.0,>=8.1.3 (installed: snakemake-interface-executor-plugins 8.1.3) Handling snakemake-interface-common <2.0,>=1.15.0 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: snakemake-interface-common <2.0,>=1.15.0 (installed: snakemake-interface-common 1.15.1) Handling snakemake-interface-storage-plugins <4.0,>=3.0.0 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: snakemake-interface-storage-plugins <4.0,>=3.0.0 (installed: snakemake-interface-storage-plugins 3.0.0) Handling stopit from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: stopit (installed: stopit 1.1.2) Handling tabulate from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: tabulate (installed: tabulate 0.9.0) Handling throttler from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: throttler (installed: throttler 1.2.2) Handling toposort >=1.10 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: toposort >=1.10 (installed: toposort 1.10) Handling wrapt from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: wrapt (installed: wrapt 1.16.0) Handling yte <2.0,>=1.5.1 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: yte <2.0,>=1.5.1 (installed: yte 1.5.4) Handling conda-inject <2.0,>=1.3.1 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: conda-inject <2.0,>=1.3.1 (installed: conda-inject 1.3.1) Handling slack-sdk ; extra == 'messaging' from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: slack-sdk ; extra == 'messaging' (installed: slack-sdk 3.26.2) Handling eido ; extra == 'pep' from hook generated metadata: Requires-Dist (snakemake) Ignoring alien requirement: eido ; extra == 'pep' Handling peppy ; extra == 'pep' from hook generated metadata: Requires-Dist (snakemake) Ignoring alien requirement: peppy ; extra == 'pep' Handling pygments ; extra == 'reports' from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: pygments ; extra == 'reports' (installed: pygments 2.17.2) + cat /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-buildrequires + rm -rfv snakemake-8.1.2.dist-info/ removed 'snakemake-8.1.2.dist-info/LICENSE.md' removed 'snakemake-8.1.2.dist-info/METADATA' removed 'snakemake-8.1.2.dist-info/top_level.txt' removed 'snakemake-8.1.2.dist-info/entry_points.txt' removed directory 'snakemake-8.1.2.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Wrote: /builddir/build/SRPMS/snakemake-8.1.2-2.fc40.buildreqs.nosrc.rpm INFO: Going to install missing dynamic buildrequires No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 25 kB/s | 1.5 kB 00:00 Additional repo http_kojipkgs_fedoraproject_org 19 kB/s | 3.8 kB 00:00 fedora 720 kB/s | 24 kB 00:00 updates 691 kB/s | 23 kB 00:00 Package python3-conda-inject-1.3.1-1.fc40.noarch is already installed. Package python3-jinja2-3.1.3-1.fc40.noarch is already installed. Package python3-pulp-2.7.0-3.fc39.noarch is already installed. Package python3-snakemake-interface-common-1.15.1-1.fc40.noarch is already installed. Package python3-snakemake-interface-executor-plugins-8.1.3-2.fc40~bootstrap.noarch is already installed. Package python3-snakemake-interface-storage-plugins-3.0.0-2.fc40~bootstrap.noarch is already installed. Package python3-yte-1.5.4-1.fc40.noarch is already installed. Package librsvg2-tools-2.57.1-1.fc40.x86_64 is already installed. Package texlive-xindy-11:svn65958-77.fc39.x86_64 is already installed. Package help2man-1.49.3-3.fc39.noarch is already installed. Package latexmk-4.82a-1.fc40.noarch is already installed. Package make-1:4.4.1-2.fc39.x86_64 is already installed. Package pyproject-rpm-macros-1.11.0-1.fc40.noarch is already installed. Package python3-devel-3.12.1-2.fc40.x86_64 is already installed. Package python3-devel-3.12.1-2.fc40.x86_64 is already installed. Package python3-sphinx-latex-1:7.2.6-4.fc40.noarch is already installed. Package python3-appdirs-1.4.4-11.fc39.noarch is already installed. Package python3-boto3-1.34.22-1.fc40.noarch is already installed. Package python3-configargparse-1.7-1.fc40.noarch is already installed. Package python3-connection_pool-0.0.3-9.fc39.noarch is already installed. Package python3-datrie-0.8.2-22.fc40.x86_64 is already installed. Package python3-docutils-0.20.1-1.fc40.noarch is already installed. Package python3-flask-1:3.0.0-1.fc40.noarch is already installed. Package python3-GitPython-3.1.40-1.fc40.noarch is already installed. Package python3-google-cloud-storage-2.14.0-2.fc40.noarch is already installed. Package python3-humanfriendly-10.0-8.fc39.noarch is already installed. Package python3-immutables-0.20-1.fc40.x86_64 is already installed. Package python3-jsonschema-4.19.1-1.fc40.noarch is already installed. Package python3-myst-parser-2.0.0-3.fc40.noarch is already installed. Package python3-nbformat-5.9.1-2.fc39.noarch is already installed. Package python3-packaging-23.2-2.fc40.noarch is already installed. Package python3-pandas-1.5.3-7.fc39~bootstrap.x86_64 is already installed. Package python3-pip-23.3.1-3.fc40.noarch is already installed. Package python3-psutil-5.9.5-2.fc40.x86_64 is already installed. Package python3-pygments-2.17.2-1.fc40.noarch is already installed. Package python3-pytest-7.4.3-1.fc40.noarch is already installed. Package python3-pyyaml-6.0.1-11.fc39.x86_64 is already installed. Package python3-requests-2.31.0-1.fc40.noarch is already installed. Package python3-reretry-0.11.8-6.fc40.noarch is already installed. Package python3-setuptools-68.2.2-1.fc40.noarch is already installed. Package python3-slackclient-3.26.2-1.fc40.noarch is already installed. Package python3-smart_open-6.4.0-1.fc40.noarch is already installed. Package python3-snakemake-executor-plugin-cluster-generic-1.0.7-1.fc40.noarch is already installed. Package python3-snakemake-interface-common-1.15.1-1.fc40.noarch is already installed. Package python3-snakemake-interface-executor-plugins-8.1.3-2.fc40~bootstrap.noarch is already installed. Package python3-snakemake-interface-storage-plugins-3.0.0-2.fc40~bootstrap.noarch is already installed. Package python3-snakemake-storage-plugin-s3-0.2.8-1.fc40.noarch is already installed. Package python3-sphinx-1:7.2.6-4.fc40.noarch is already installed. Package python3-sphinx-argparse-0.4.0-4.fc39.noarch is already installed. Package python3-stopit-1.1.2-8.fc39.noarch is already installed. Package python3-tabulate-0.9.0-4.fc39.noarch is already installed. Package python3-throttler-1.2.2-7.fc40.noarch is already installed. Package python3-toposort-1.10-8.fc40.noarch is already installed. Package python3-wheel-1:0.41.2-1.fc40.noarch is already installed. Package python3-wrapt-1.16.0-1.fc40.x86_64 is already installed. Package texlive-xetex-11:svn66203-77.fc39.x86_64 is already installed. Package vim-filesystem-2:9.1.031-1.fc40.noarch is already installed. Dependencies resolved. Nothing to do. Complete! Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1705622400 Executing(%generate_buildrequires): /bin/sh -e /var/tmp/rpm-tmp.DUZuFZ + umask 022 + cd /builddir/build/BUILD + cd snakemake-8.1.2 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + echo pyproject-rpm-macros + echo python3-devel + echo 'python3dist(pip) >= 19' + echo 'python3dist(packaging)' + '[' -f pyproject.toml ']' + echo '(python3dist(tomli) if python3-devel < 3.11)' + rm -rfv '*.dist-info/' + '[' -f /usr/bin/python3 ']' + mkdir -p /builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir + echo -n + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 ' + TMPDIR=/builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir + RPM_TOXENV=py312 + HOSTNAME=rpmbuild + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_buildrequires.py --generate-extras --python3_pkgversion 3 --wheeldir /builddir/build/BUILD/snakemake-8.1.2/pyproject-wheeldir --output /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-buildrequires -x reports,messaging,google-cloud,azure docs/requirements.txt Handling sphinx >=3 from requirements file docs/requirements.txt Requirement satisfied: sphinx >=3 (installed: sphinx 7.2.6) Handling sphinx-argparse from requirements file docs/requirements.txt Requirement satisfied: sphinx-argparse (installed: sphinx-argparse 0.4.0) Handling docutils from requirements file docs/requirements.txt Requirement satisfied: docutils (installed: docutils 0.20.1) Handling myst-parser from requirements file docs/requirements.txt Requirement satisfied: myst-parser (installed: myst-parser 2.0.0) Handling configargparse from requirements file docs/requirements.txt Requirement satisfied: configargparse (installed: configargparse 1.7) Handling appdirs from requirements file docs/requirements.txt Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling snakemake-interface-common from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-common (installed: snakemake-interface-common 1.15.1) Handling snakemake-interface-executor-plugins from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-executor-plugins (installed: snakemake-interface-executor-plugins 8.1.3) Handling snakemake-interface-storage-plugins from requirements file docs/requirements.txt Requirement satisfied: snakemake-interface-storage-plugins (installed: snakemake-interface-storage-plugins 3.0.0) Handling setuptools>=42 from build-system.requires Requirement satisfied: setuptools>=42 (installed: setuptools 68.2.2) Handling tomli; python_version < "3.11" from build-system.requires Ignoring alien requirement: tomli; python_version < "3.11" running egg_info writing snakemake.egg-info/PKG-INFO writing dependency_links to snakemake.egg-info/dependency_links.txt writing entry points to snakemake.egg-info/entry_points.txt writing requirements to snakemake.egg-info/requires.txt writing top-level names to snakemake.egg-info/top_level.txt reading manifest file 'snakemake.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.md' writing manifest file 'snakemake.egg-info/SOURCES.txt' Handling wheel from get_requires_for_build_wheel Requirement satisfied: wheel (installed: wheel 0.41.2) running dist_info writing snakemake.egg-info/PKG-INFO writing dependency_links to snakemake.egg-info/dependency_links.txt writing entry points to snakemake.egg-info/entry_points.txt writing requirements to snakemake.egg-info/requires.txt writing top-level names to snakemake.egg-info/top_level.txt reading manifest file 'snakemake.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.md' writing manifest file 'snakemake.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/snakemake-8.1.2/snakemake-8.1.2.dist-info' Handling appdirs from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: appdirs (installed: appdirs 1.4.4) Handling immutables from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: immutables (installed: immutables 0.20) Handling configargparse from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: configargparse (installed: configargparse 1.7) Handling connection-pool >=0.0.3 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: connection-pool >=0.0.3 (installed: connection-pool 0.0.3) Handling datrie from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: datrie (installed: datrie 0.8.2) Handling docutils from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: docutils (installed: docutils 0.20.1) Handling gitpython from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: gitpython (installed: gitpython 3.1.40) Handling humanfriendly from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: humanfriendly (installed: humanfriendly 10.0) Handling jinja2 <4.0,>=3.0 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: jinja2 <4.0,>=3.0 (installed: jinja2 3.1.3) Handling jsonschema from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: jsonschema (installed: jsonschema 4.19.1) Handling nbformat from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: nbformat (installed: nbformat 5.9.1) Handling packaging from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: packaging (installed: packaging 23.2) Handling psutil from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: psutil (installed: psutil 5.9.5) Handling pulp <2.9,>=2.3.1 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: pulp <2.9,>=2.3.1 (installed: pulp 2.7.0) Handling pyyaml from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: pyyaml (installed: pyyaml 6.0.1) Handling requests from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: requests (installed: requests 2.31.0) Handling reretry from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: reretry (installed: reretry 0.11.8) Handling smart-open >=3.0 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: smart-open >=3.0 (installed: smart-open 6.4.0) Handling snakemake-interface-executor-plugins <9.0,>=8.1.3 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: snakemake-interface-executor-plugins <9.0,>=8.1.3 (installed: snakemake-interface-executor-plugins 8.1.3) Handling snakemake-interface-common <2.0,>=1.15.0 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: snakemake-interface-common <2.0,>=1.15.0 (installed: snakemake-interface-common 1.15.1) Handling snakemake-interface-storage-plugins <4.0,>=3.0.0 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: snakemake-interface-storage-plugins <4.0,>=3.0.0 (installed: snakemake-interface-storage-plugins 3.0.0) Handling stopit from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: stopit (installed: stopit 1.1.2) Handling tabulate from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: tabulate (installed: tabulate 0.9.0) Handling throttler from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: throttler (installed: throttler 1.2.2) Handling toposort >=1.10 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: toposort >=1.10 (installed: toposort 1.10) Handling wrapt from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: wrapt (installed: wrapt 1.16.0) Handling yte <2.0,>=1.5.1 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: yte <2.0,>=1.5.1 (installed: yte 1.5.4) Handling conda-inject <2.0,>=1.3.1 from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: conda-inject <2.0,>=1.3.1 (installed: conda-inject 1.3.1) Handling slack-sdk ; extra == 'messaging' from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: slack-sdk ; extra == 'messaging' (installed: slack-sdk 3.26.2) Handling eido ; extra == 'pep' from hook generated metadata: Requires-Dist (snakemake) Ignoring alien requirement: eido ; extra == 'pep' Handling peppy ; extra == 'pep' from hook generated metadata: Requires-Dist (snakemake) Ignoring alien requirement: peppy ; extra == 'pep' Handling pygments ; extra == 'reports' from hook generated metadata: Requires-Dist (snakemake) Requirement satisfied: pygments ; extra == 'reports' (installed: pygments 2.17.2) + cat /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-buildrequires + rm -rfv snakemake-8.1.2.dist-info/ removed 'snakemake-8.1.2.dist-info/LICENSE.md' removed 'snakemake-8.1.2.dist-info/METADATA' removed 'snakemake-8.1.2.dist-info/entry_points.txt' removed 'snakemake-8.1.2.dist-info/top_level.txt' removed directory 'snakemake-8.1.2.dist-info/' + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.vdePKO + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd snakemake-8.1.2 + mkdir -p /builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + TMPDIR=/builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir + /usr/bin/python3 -Bs /usr/lib/rpm/redhat/pyproject_wheel.py /builddir/build/BUILD/snakemake-8.1.2/pyproject-wheeldir Processing /builddir/build/BUILD/snakemake-8.1.2 Preparing metadata (pyproject.toml): started Running command Preparing metadata (pyproject.toml) running dist_info creating /builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir/pip-modern-metadata-n6jfd0yf/snakemake.egg-info writing /builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir/pip-modern-metadata-n6jfd0yf/snakemake.egg-info/PKG-INFO writing dependency_links to /builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir/pip-modern-metadata-n6jfd0yf/snakemake.egg-info/dependency_links.txt writing entry points to /builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir/pip-modern-metadata-n6jfd0yf/snakemake.egg-info/entry_points.txt writing requirements to /builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir/pip-modern-metadata-n6jfd0yf/snakemake.egg-info/requires.txt writing top-level names to /builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir/pip-modern-metadata-n6jfd0yf/snakemake.egg-info/top_level.txt writing manifest file '/builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir/pip-modern-metadata-n6jfd0yf/snakemake.egg-info/SOURCES.txt' reading manifest file '/builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir/pip-modern-metadata-n6jfd0yf/snakemake.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.md' writing manifest file '/builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir/pip-modern-metadata-n6jfd0yf/snakemake.egg-info/SOURCES.txt' creating '/builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir/pip-modern-metadata-n6jfd0yf/snakemake-8.1.2.dist-info' Preparing metadata (pyproject.toml): finished with status 'done' Building wheels for collected packages: snakemake Building wheel for snakemake (pyproject.toml): started Running command Building wheel for snakemake (pyproject.toml) running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/snakemake copying snakemake/wrapper.py -> build/lib/snakemake copying snakemake/workflow.py -> build/lib/snakemake copying snakemake/utils.py -> build/lib/snakemake copying snakemake/target_jobs.py -> build/lib/snakemake copying snakemake/storage.py -> build/lib/snakemake copying snakemake/spawn_jobs.py -> build/lib/snakemake copying snakemake/sourcecache.py -> build/lib/snakemake copying snakemake/shell.py -> build/lib/snakemake copying snakemake/settings.py -> build/lib/snakemake copying snakemake/scheduler.py -> build/lib/snakemake copying snakemake/rules.py -> build/lib/snakemake copying snakemake/ruleinfo.py -> build/lib/snakemake copying snakemake/resources.py -> build/lib/snakemake copying snakemake/profiles.py -> build/lib/snakemake copying snakemake/persistence.py -> build/lib/snakemake copying snakemake/path_modifier.py -> build/lib/snakemake copying snakemake/parser.py -> build/lib/snakemake copying snakemake/output_index.py -> build/lib/snakemake copying snakemake/notebook.py -> build/lib/snakemake copying snakemake/modules.py -> build/lib/snakemake copying snakemake/logging.py -> build/lib/snakemake copying snakemake/jobs.py -> build/lib/snakemake copying snakemake/io.py -> build/lib/snakemake copying snakemake/gui.py -> build/lib/snakemake copying snakemake/exceptions.py -> build/lib/snakemake copying snakemake/decorators.py -> build/lib/snakemake copying snakemake/dag.py -> build/lib/snakemake copying snakemake/cwl.py -> build/lib/snakemake copying snakemake/cli.py -> build/lib/snakemake copying snakemake/checkpoints.py -> build/lib/snakemake copying snakemake/benchmark.py -> build/lib/snakemake copying snakemake/api.py -> build/lib/snakemake copying snakemake/_version.py -> build/lib/snakemake copying snakemake/__main__.py -> build/lib/snakemake copying snakemake/__init__.py -> build/lib/snakemake creating build/lib/snakemake/unit_tests copying snakemake/unit_tests/__init__.py -> build/lib/snakemake/unit_tests creating build/lib/snakemake/template_rendering copying snakemake/template_rendering/yte.py -> build/lib/snakemake/template_rendering copying snakemake/template_rendering/jinja2.py -> build/lib/snakemake/template_rendering copying snakemake/template_rendering/__init__.py -> build/lib/snakemake/template_rendering creating build/lib/snakemake/script copying snakemake/script/__init__.py -> build/lib/snakemake/script creating build/lib/snakemake/report copying snakemake/report/rulegraph_spec.py -> build/lib/snakemake/report copying snakemake/report/__init__.py -> build/lib/snakemake/report creating build/lib/snakemake/remote copying snakemake/remote/zenodo.py -> build/lib/snakemake/remote copying snakemake/remote/webdav.py -> build/lib/snakemake/remote copying snakemake/remote/iRODS.py -> build/lib/snakemake/remote copying snakemake/remote/gridftp.py -> build/lib/snakemake/remote copying snakemake/remote/gfal.py -> build/lib/snakemake/remote copying snakemake/remote/dropbox.py -> build/lib/snakemake/remote copying snakemake/remote/__init__.py -> build/lib/snakemake/remote copying snakemake/remote/XRootD.py -> build/lib/snakemake/remote copying snakemake/remote/SFTP.py -> build/lib/snakemake/remote copying snakemake/remote/S3Mocked.py -> build/lib/snakemake/remote copying snakemake/remote/S3.py -> build/lib/snakemake/remote copying snakemake/remote/NCBI.py -> build/lib/snakemake/remote copying snakemake/remote/HTTP.py -> build/lib/snakemake/remote copying snakemake/remote/GS.py -> build/lib/snakemake/remote copying snakemake/remote/FTP.py -> build/lib/snakemake/remote copying snakemake/remote/EGA.py -> build/lib/snakemake/remote copying snakemake/remote/AzBlob.py -> build/lib/snakemake/remote creating build/lib/snakemake/linting copying snakemake/linting/snakefiles.py -> build/lib/snakemake/linting copying snakemake/linting/rules.py -> build/lib/snakemake/linting copying snakemake/linting/links.py -> build/lib/snakemake/linting copying snakemake/linting/__init__.py -> build/lib/snakemake/linting creating build/lib/snakemake/executors copying snakemake/executors/google_lifesciences_helper.py -> build/lib/snakemake/executors copying snakemake/executors/touch.py -> build/lib/snakemake/executors copying snakemake/executors/local.py -> build/lib/snakemake/executors copying snakemake/executors/dryrun.py -> build/lib/snakemake/executors copying snakemake/executors/__init__.py -> build/lib/snakemake/executors creating build/lib/snakemake/deployment copying snakemake/deployment/singularity.py -> build/lib/snakemake/deployment copying snakemake/deployment/env_modules.py -> build/lib/snakemake/deployment copying snakemake/deployment/containerize.py -> build/lib/snakemake/deployment copying snakemake/deployment/conda.py -> build/lib/snakemake/deployment copying snakemake/deployment/__init__.py -> build/lib/snakemake/deployment creating build/lib/snakemake/common copying snakemake/common/workdir_handler.py -> build/lib/snakemake/common copying snakemake/common/tbdstring.py -> build/lib/snakemake/common copying snakemake/common/git.py -> build/lib/snakemake/common copying snakemake/common/configfile.py -> build/lib/snakemake/common copying snakemake/common/argparse.py -> build/lib/snakemake/common copying snakemake/common/__init__.py -> build/lib/snakemake/common creating build/lib/snakemake/caching copying snakemake/caching/storage.py -> build/lib/snakemake/caching copying snakemake/caching/local.py -> build/lib/snakemake/caching copying snakemake/caching/hash.py -> build/lib/snakemake/caching copying snakemake/caching/__init__.py -> build/lib/snakemake/caching creating build/lib/snakemake/unit_tests/templates copying snakemake/unit_tests/templates/__init__.py -> build/lib/snakemake/unit_tests/templates creating build/lib/snakemake/report/template copying snakemake/report/template/__init__.py -> build/lib/snakemake/report/template creating build/lib/snakemake/report/data copying snakemake/report/data/timeline.py -> build/lib/snakemake/report/data copying snakemake/report/data/runtimes.py -> build/lib/snakemake/report/data copying snakemake/report/data/rules.py -> build/lib/snakemake/report/data copying snakemake/report/data/rulegraph.py -> build/lib/snakemake/report/data copying snakemake/report/data/results.py -> build/lib/snakemake/report/data copying snakemake/report/data/packages.py -> build/lib/snakemake/report/data copying snakemake/report/data/common.py -> build/lib/snakemake/report/data copying snakemake/report/data/categories.py -> build/lib/snakemake/report/data copying snakemake/report/data/__init__.py -> build/lib/snakemake/report/data creating build/lib/snakemake/report/template/components copying snakemake/report/template/components/__init__.py -> build/lib/snakemake/report/template/components creating build/lib/snakemake/common/tests copying snakemake/common/tests/__init__.py -> build/lib/snakemake/common/tests creating build/lib/snakemake/common/tests/testcases copying snakemake/common/tests/testcases/__init__.py -> build/lib/snakemake/common/tests/testcases creating build/lib/snakemake/common/tests/testcases/simple copying snakemake/common/tests/testcases/simple/__init__.py -> build/lib/snakemake/common/tests/testcases/simple creating build/lib/snakemake/common/tests/testcases/groups copying snakemake/common/tests/testcases/groups/__init__.py -> build/lib/snakemake/common/tests/testcases/groups copying snakemake/report.css -> build/lib/snakemake copying snakemake/gui.html -> build/lib/snakemake copying snakemake/executors/jobscript.sh -> build/lib/snakemake/executors copying snakemake/unit_tests/templates/ruletest.py.jinja2 -> build/lib/snakemake/unit_tests/templates copying snakemake/unit_tests/templates/common.py.jinja2 -> build/lib/snakemake/unit_tests/templates copying snakemake/report/template/style.css -> build/lib/snakemake/report/template copying snakemake/report/template/index.html.jinja2 -> build/lib/snakemake/report/template copying snakemake/report/template/logo.svg -> build/lib/snakemake/report/template copying snakemake/report/template/components/subcategory.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/stats.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/search_results.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/rule_info.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/rule_graph.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/result_view_button.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/result_info.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/report_info.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/navbar.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/menu.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/list_item.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/list_heading.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/icon.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/content.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/common.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/category.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/button.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/breadcrumbs.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/app.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/abstract_results.js -> build/lib/snakemake/report/template/components copying snakemake/report/template/components/abstract_menu.js -> build/lib/snakemake/report/template/components copying snakemake/common/tests/testcases/simple/Snakefile -> build/lib/snakemake/common/tests/testcases/simple copying snakemake/common/tests/testcases/groups/Snakefile -> build/lib/snakemake/common/tests/testcases/groups UPDATING build/lib/snakemake/_version.py set build/lib/snakemake/_version.py to '8.1.2' installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/_version.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/gui.html -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/report.css -> build/bdist.linux-x86_64/wheel/snakemake creating build/bdist.linux-x86_64/wheel/snakemake/caching copying build/lib/snakemake/caching/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/caching copying build/lib/snakemake/caching/hash.py -> build/bdist.linux-x86_64/wheel/snakemake/caching copying build/lib/snakemake/caching/local.py -> build/bdist.linux-x86_64/wheel/snakemake/caching copying build/lib/snakemake/caching/storage.py -> build/bdist.linux-x86_64/wheel/snakemake/caching creating build/bdist.linux-x86_64/wheel/snakemake/common creating build/bdist.linux-x86_64/wheel/snakemake/common/tests creating build/bdist.linux-x86_64/wheel/snakemake/common/tests/testcases creating build/bdist.linux-x86_64/wheel/snakemake/common/tests/testcases/groups copying build/lib/snakemake/common/tests/testcases/groups/Snakefile -> build/bdist.linux-x86_64/wheel/snakemake/common/tests/testcases/groups copying build/lib/snakemake/common/tests/testcases/groups/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/common/tests/testcases/groups creating build/bdist.linux-x86_64/wheel/snakemake/common/tests/testcases/simple copying build/lib/snakemake/common/tests/testcases/simple/Snakefile -> build/bdist.linux-x86_64/wheel/snakemake/common/tests/testcases/simple copying build/lib/snakemake/common/tests/testcases/simple/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/common/tests/testcases/simple copying build/lib/snakemake/common/tests/testcases/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/common/tests/testcases copying build/lib/snakemake/common/tests/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/common/tests copying build/lib/snakemake/common/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/common copying build/lib/snakemake/common/argparse.py -> build/bdist.linux-x86_64/wheel/snakemake/common copying build/lib/snakemake/common/configfile.py -> build/bdist.linux-x86_64/wheel/snakemake/common copying build/lib/snakemake/common/git.py -> build/bdist.linux-x86_64/wheel/snakemake/common copying build/lib/snakemake/common/tbdstring.py -> build/bdist.linux-x86_64/wheel/snakemake/common copying build/lib/snakemake/common/workdir_handler.py -> build/bdist.linux-x86_64/wheel/snakemake/common creating build/bdist.linux-x86_64/wheel/snakemake/deployment copying build/lib/snakemake/deployment/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/deployment copying build/lib/snakemake/deployment/conda.py -> build/bdist.linux-x86_64/wheel/snakemake/deployment copying build/lib/snakemake/deployment/containerize.py -> build/bdist.linux-x86_64/wheel/snakemake/deployment copying build/lib/snakemake/deployment/env_modules.py -> build/bdist.linux-x86_64/wheel/snakemake/deployment copying build/lib/snakemake/deployment/singularity.py -> build/bdist.linux-x86_64/wheel/snakemake/deployment creating build/bdist.linux-x86_64/wheel/snakemake/executors copying build/lib/snakemake/executors/jobscript.sh -> build/bdist.linux-x86_64/wheel/snakemake/executors copying build/lib/snakemake/executors/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/executors copying build/lib/snakemake/executors/dryrun.py -> build/bdist.linux-x86_64/wheel/snakemake/executors copying build/lib/snakemake/executors/local.py -> build/bdist.linux-x86_64/wheel/snakemake/executors copying build/lib/snakemake/executors/touch.py -> build/bdist.linux-x86_64/wheel/snakemake/executors copying build/lib/snakemake/executors/google_lifesciences_helper.py -> build/bdist.linux-x86_64/wheel/snakemake/executors creating build/bdist.linux-x86_64/wheel/snakemake/linting copying build/lib/snakemake/linting/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/linting copying build/lib/snakemake/linting/links.py -> build/bdist.linux-x86_64/wheel/snakemake/linting copying build/lib/snakemake/linting/rules.py -> build/bdist.linux-x86_64/wheel/snakemake/linting copying build/lib/snakemake/linting/snakefiles.py -> build/bdist.linux-x86_64/wheel/snakemake/linting creating build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/AzBlob.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/EGA.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/FTP.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/GS.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/HTTP.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/NCBI.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/S3.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/S3Mocked.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/SFTP.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/XRootD.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/dropbox.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/gfal.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/gridftp.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/iRODS.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/webdav.py -> build/bdist.linux-x86_64/wheel/snakemake/remote copying build/lib/snakemake/remote/zenodo.py -> build/bdist.linux-x86_64/wheel/snakemake/remote creating build/bdist.linux-x86_64/wheel/snakemake/report creating build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/categories.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/common.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/packages.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/results.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/rulegraph.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/rules.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/runtimes.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data copying build/lib/snakemake/report/data/timeline.py -> build/bdist.linux-x86_64/wheel/snakemake/report/data creating build/bdist.linux-x86_64/wheel/snakemake/report/template copying build/lib/snakemake/report/template/logo.svg -> build/bdist.linux-x86_64/wheel/snakemake/report/template copying build/lib/snakemake/report/template/index.html.jinja2 -> build/bdist.linux-x86_64/wheel/snakemake/report/template copying build/lib/snakemake/report/template/style.css -> build/bdist.linux-x86_64/wheel/snakemake/report/template creating build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/abstract_menu.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/abstract_results.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/app.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/breadcrumbs.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/button.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/category.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/common.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/content.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/icon.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/list_heading.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/list_item.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/menu.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/navbar.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/report_info.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/result_info.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/result_view_button.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/rule_graph.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/rule_info.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/search_results.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/stats.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/subcategory.js -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/components/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/report/template/components copying build/lib/snakemake/report/template/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/report/template copying build/lib/snakemake/report/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/report copying build/lib/snakemake/report/rulegraph_spec.py -> build/bdist.linux-x86_64/wheel/snakemake/report creating build/bdist.linux-x86_64/wheel/snakemake/script copying build/lib/snakemake/script/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/script creating build/bdist.linux-x86_64/wheel/snakemake/template_rendering copying build/lib/snakemake/template_rendering/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/template_rendering copying build/lib/snakemake/template_rendering/jinja2.py -> build/bdist.linux-x86_64/wheel/snakemake/template_rendering copying build/lib/snakemake/template_rendering/yte.py -> build/bdist.linux-x86_64/wheel/snakemake/template_rendering creating build/bdist.linux-x86_64/wheel/snakemake/unit_tests creating build/bdist.linux-x86_64/wheel/snakemake/unit_tests/templates copying build/lib/snakemake/unit_tests/templates/common.py.jinja2 -> build/bdist.linux-x86_64/wheel/snakemake/unit_tests/templates copying build/lib/snakemake/unit_tests/templates/ruletest.py.jinja2 -> build/bdist.linux-x86_64/wheel/snakemake/unit_tests/templates copying build/lib/snakemake/unit_tests/templates/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/unit_tests/templates copying build/lib/snakemake/unit_tests/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake/unit_tests copying build/lib/snakemake/__init__.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/__main__.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/api.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/benchmark.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/checkpoints.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/cli.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/cwl.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/dag.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/decorators.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/exceptions.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/gui.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/io.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/jobs.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/logging.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/modules.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/notebook.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/output_index.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/parser.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/path_modifier.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/persistence.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/profiles.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/resources.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/ruleinfo.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/rules.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/scheduler.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/settings.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/shell.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/sourcecache.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/spawn_jobs.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/storage.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/target_jobs.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/utils.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/workflow.py -> build/bdist.linux-x86_64/wheel/snakemake copying build/lib/snakemake/wrapper.py -> build/bdist.linux-x86_64/wheel/snakemake running install_egg_info running egg_info writing snakemake.egg-info/PKG-INFO writing dependency_links to snakemake.egg-info/dependency_links.txt writing entry points to snakemake.egg-info/entry_points.txt writing requirements to snakemake.egg-info/requires.txt writing top-level names to snakemake.egg-info/top_level.txt reading manifest file 'snakemake.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.md' writing manifest file 'snakemake.egg-info/SOURCES.txt' Copying snakemake.egg-info to build/bdist.linux-x86_64/wheel/snakemake-8.1.2-py3.12.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/snakemake-8.1.2.dist-info/WHEEL creating '/builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir/pip-wheel-wjh6e0o4/.tmp-c4gj1mk6/snakemake-8.1.2-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'snakemake/__init__.py' adding 'snakemake/__main__.py' adding 'snakemake/_version.py' adding 'snakemake/api.py' adding 'snakemake/benchmark.py' adding 'snakemake/checkpoints.py' adding 'snakemake/cli.py' adding 'snakemake/cwl.py' adding 'snakemake/dag.py' adding 'snakemake/decorators.py' adding 'snakemake/exceptions.py' adding 'snakemake/gui.html' adding 'snakemake/gui.py' adding 'snakemake/io.py' adding 'snakemake/jobs.py' adding 'snakemake/logging.py' adding 'snakemake/modules.py' adding 'snakemake/notebook.py' adding 'snakemake/output_index.py' adding 'snakemake/parser.py' adding 'snakemake/path_modifier.py' adding 'snakemake/persistence.py' adding 'snakemake/profiles.py' adding 'snakemake/report.css' adding 'snakemake/resources.py' adding 'snakemake/ruleinfo.py' adding 'snakemake/rules.py' adding 'snakemake/scheduler.py' adding 'snakemake/settings.py' adding 'snakemake/shell.py' adding 'snakemake/sourcecache.py' adding 'snakemake/spawn_jobs.py' adding 'snakemake/storage.py' adding 'snakemake/target_jobs.py' adding 'snakemake/utils.py' adding 'snakemake/workflow.py' adding 'snakemake/wrapper.py' adding 'snakemake/caching/__init__.py' adding 'snakemake/caching/hash.py' adding 'snakemake/caching/local.py' adding 'snakemake/caching/storage.py' adding 'snakemake/common/__init__.py' adding 'snakemake/common/argparse.py' adding 'snakemake/common/configfile.py' adding 'snakemake/common/git.py' adding 'snakemake/common/tbdstring.py' adding 'snakemake/common/workdir_handler.py' adding 'snakemake/common/tests/__init__.py' adding 'snakemake/common/tests/testcases/__init__.py' adding 'snakemake/common/tests/testcases/groups/Snakefile' adding 'snakemake/common/tests/testcases/groups/__init__.py' adding 'snakemake/common/tests/testcases/simple/Snakefile' adding 'snakemake/common/tests/testcases/simple/__init__.py' adding 'snakemake/deployment/__init__.py' adding 'snakemake/deployment/conda.py' adding 'snakemake/deployment/containerize.py' adding 'snakemake/deployment/env_modules.py' adding 'snakemake/deployment/singularity.py' adding 'snakemake/executors/__init__.py' adding 'snakemake/executors/dryrun.py' adding 'snakemake/executors/google_lifesciences_helper.py' adding 'snakemake/executors/jobscript.sh' adding 'snakemake/executors/local.py' adding 'snakemake/executors/touch.py' adding 'snakemake/linting/__init__.py' adding 'snakemake/linting/links.py' adding 'snakemake/linting/rules.py' adding 'snakemake/linting/snakefiles.py' adding 'snakemake/remote/AzBlob.py' adding 'snakemake/remote/EGA.py' adding 'snakemake/remote/FTP.py' adding 'snakemake/remote/GS.py' adding 'snakemake/remote/HTTP.py' adding 'snakemake/remote/NCBI.py' adding 'snakemake/remote/S3.py' adding 'snakemake/remote/S3Mocked.py' adding 'snakemake/remote/SFTP.py' adding 'snakemake/remote/XRootD.py' adding 'snakemake/remote/__init__.py' adding 'snakemake/remote/dropbox.py' adding 'snakemake/remote/gfal.py' adding 'snakemake/remote/gridftp.py' adding 'snakemake/remote/iRODS.py' adding 'snakemake/remote/webdav.py' adding 'snakemake/remote/zenodo.py' adding 'snakemake/report/__init__.py' adding 'snakemake/report/rulegraph_spec.py' adding 'snakemake/report/data/__init__.py' adding 'snakemake/report/data/categories.py' adding 'snakemake/report/data/common.py' adding 'snakemake/report/data/packages.py' adding 'snakemake/report/data/results.py' adding 'snakemake/report/data/rulegraph.py' adding 'snakemake/report/data/rules.py' adding 'snakemake/report/data/runtimes.py' adding 'snakemake/report/data/timeline.py' adding 'snakemake/report/template/__init__.py' adding 'snakemake/report/template/index.html.jinja2' adding 'snakemake/report/template/logo.svg' adding 'snakemake/report/template/style.css' adding 'snakemake/report/template/components/__init__.py' adding 'snakemake/report/template/components/abstract_menu.js' adding 'snakemake/report/template/components/abstract_results.js' adding 'snakemake/report/template/components/app.js' adding 'snakemake/report/template/components/breadcrumbs.js' adding 'snakemake/report/template/components/button.js' adding 'snakemake/report/template/components/category.js' adding 'snakemake/report/template/components/common.js' adding 'snakemake/report/template/components/content.js' adding 'snakemake/report/template/components/icon.js' adding 'snakemake/report/template/components/list_heading.js' adding 'snakemake/report/template/components/list_item.js' adding 'snakemake/report/template/components/menu.js' adding 'snakemake/report/template/components/navbar.js' adding 'snakemake/report/template/components/report_info.js' adding 'snakemake/report/template/components/result_info.js' adding 'snakemake/report/template/components/result_view_button.js' adding 'snakemake/report/template/components/rule_graph.js' adding 'snakemake/report/template/components/rule_info.js' adding 'snakemake/report/template/components/search_results.js' adding 'snakemake/report/template/components/stats.js' adding 'snakemake/report/template/components/subcategory.js' adding 'snakemake/script/__init__.py' adding 'snakemake/template_rendering/__init__.py' adding 'snakemake/template_rendering/jinja2.py' adding 'snakemake/template_rendering/yte.py' adding 'snakemake/unit_tests/__init__.py' adding 'snakemake/unit_tests/templates/__init__.py' adding 'snakemake/unit_tests/templates/common.py.jinja2' adding 'snakemake/unit_tests/templates/ruletest.py.jinja2' adding 'snakemake-8.1.2.dist-info/LICENSE.md' adding 'snakemake-8.1.2.dist-info/METADATA' adding 'snakemake-8.1.2.dist-info/WHEEL' adding 'snakemake-8.1.2.dist-info/entry_points.txt' adding 'snakemake-8.1.2.dist-info/top_level.txt' adding 'snakemake-8.1.2.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Building wheel for snakemake (pyproject.toml): finished with status 'done' Created wheel for snakemake: filename=snakemake-8.1.2-py3-none-any.whl size=285575 sha256=4310097bdd9f41c72d7541a11bd198c6d9b718c1e3a2e49e77dbbe891e0d78bb Stored in directory: /builddir/.cache/pip/wheels/02/45/62/2b49ebfc1f81061159237915f67e41e48927bc21d5f3141ba2 Successfully built snakemake + read -r fn + find docs -type f -name '*.svg' ++ dirname docs/_static/logo-snake.svg ++ basename docs/_static/logo-snake.svg .svg + rsvg-convert --format=pdf --output=docs/_static/logo-snake.pdf docs/_static/logo-snake.svg + read -r fn + find docs/executor_tutorial -type f -exec gawk '/\.svg/ { print FILENAME; nextfile }' '{}' + + xargs -r -t sed -r -i 's/(image::.*)\.svg/\1\.pdf/' find: ‘docs/executor_tutorial’: No such file or directory + PYTHONPATH=/builddir/build/BUILD/snakemake-8.1.2 + /usr/bin/make -O -j2 V=1 VERBOSE=1 -C docs latexpdf 'SPHINXOPTS=-j${RPM_BUILD_NCPUS}' make: Entering directory '/builddir/build/BUILD/snakemake-8.1.2/docs' sphinx-build -b latex -d _build/doctrees -j2 . _build/latex Running Sphinx v7.2.6 making output directory... done myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) building [mo]: targets for 0 po files that are out of date writing output... building [latex]: all documents updating environment: [new config] 32 added, 0 changed, 0 removed reading sources... [100%] snakefiles/utils .. tutorial/tutorial looking for now-outdated files... none found pickling environment... done checking consistency... done copying TeX support files... copying TeX support files... done processing Snakemake.tex... index getting_started/installation getting_started/migration snakefiles/best_practices tutorial/tutorial tutorial/setup tutorial/basics tutorial/advanced tutorial/additional_features executing/cli executing/grouping executing/caching executing/interoperability executing/monitoring snakefiles/writing_snakefiles snakefiles/rules snakefiles/configuration snakefiles/modularization snakefiles/storage snakefiles/utils snakefiles/deployment snakefiles/reporting snakefiles/testing snakefiles/foreign_wms project_info/citations project_info/more_resources project_info/faq project_info/contributing project_info/authors project_info/history project_info/license resolving references... done writing... done copying images... [100%] project_info/img/idea.png build succeeded, 479 warnings. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). Running LaTeX files through pdflatex... /builddir/build/BUILD/snakemake-8.1.2/docs/executing/cli.rst:71: WARNING: Explicit markup ends without a blank line; unexpected unindent. /builddir/build/BUILD/snakemake-8.1.2/docs/executing/cli.rst:206: CRITICAL: Title level inconsistent: Use templating in profiles ~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/snakemake-8.1.2/docs/executing/cli.rst:112: WARNING: duplicate label profiles, other instance in /builddir/build/BUILD/snakemake-8.1.2/docs/executing/cli.rst /builddir/build/BUILD/snakemake-8.1.2/docs/executing/monitoring.rst:5: WARNING: duplicate label monitoring, other instance in /builddir/build/BUILD/snakemake-8.1.2/docs/executing/monitoring.rst /builddir/build/BUILD/snakemake-8.1.2/docs/getting_started/migration.rst:5: WARNING: Duplicate explicit target name: "snakemake plugin catalog". /builddir/build/BUILD/snakemake-8.1.2/docs/getting_started/migration.rst:5: WARNING: Duplicate explicit target name: "here". 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/builddir/build/BUILD/snakemake-8.1.2/docs/project_info/faq.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-8.1.2/docs/project_info/faq.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-8.1.2/docs/project_info/faq.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-8.1.2/docs/project_info/faq.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-8.1.2/docs/project_info/faq.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-8.1.2/docs/tutorial/advanced.rst:82: WARNING: duplicate label exercise, other instance in /builddir/build/BUILD/snakemake-8.1.2/docs/tutorial/additional_features.rst /builddir/build/BUILD/snakemake-8.1.2/docs/tutorial/advanced.rst:177: WARNING: duplicate label exercise, other instance in /builddir/build/BUILD/snakemake-8.1.2/docs/tutorial/advanced.rst 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/builddir/build/BUILD/snakemake-8.1.2/docs/snakefiles/best_practices.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-8.1.2/docs/snakefiles/configuration.rst:55: WARNING: malformed hyperlink target. /builddir/build/BUILD/snakemake-8.1.2/docs/snakefiles/modularization.rst:7: WARNING: Duplicate explicit target name: "cwl". /builddir/build/BUILD/snakemake-8.1.2/docs/snakefiles/reporting.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-8.1.2/docs/snakefiles/reporting.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-8.1.2/docs/snakefiles/rules.rst:5: WARNING: Duplicate explicit target name: "humanfriendly package". /builddir/build/BUILD/snakemake-8.1.2/docs/snakefiles/rules.rst:5: WARNING: Duplicate explicit target name: "here". /builddir/build/BUILD/snakemake-8.1.2/docs/tutorial/short.rst: WARNING: document isn't included in any toctree /builddir/build/BUILD/snakemake-8.1.2/docs/snakefiles/best_practices.rst:22: WARNING: undefined label: 'snakefiles_tabular_configuration' /builddir/build/BUILD/snakemake-8.1.2/docs/snakefiles/best_practices.rst:22: WARNING: undefined label: 'snakefiles_peps' /builddir/build/BUILD/snakemake-8.1.2/docs/tutorial/basics.rst:394: WARNING: undefined label: '.. _snakefiles-rules' /builddir/build/BUILD/snakemake-8.1.2/docs/tutorial/additional_features.rst:82: WARNING: undefined label: 'snakefiles-sub_workflows' /builddir/build/BUILD/snakemake-8.1.2/docs/executing/caching.rst:23: WARNING: undefined label: 'cloud' /builddir/build/BUILD/snakemake-8.1.2/docs/snakefiles/configuration.rst:35: WARNING: undefined label: 'api_reference_snakemake' /builddir/build/BUILD/snakemake-8.1.2/docs/snakefiles/utils.rst:7: WARNING: undefined label: 'utils-api' /builddir/build/BUILD/snakemake-8.1.2/docs/snakefiles/foreign_wms.rst:30: WARNING: undefined label: 'snakefiles-local-rule' WARNING: Could not fetch remote image: https://img.shields.io/badge/Gitpod-ready--to--code-blue?color=%23022c22 [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Gitpod-ready--to--code-blue?color=%23022c22 (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] WARNING: Could not fetch remote image: https://img.shields.io/conda/dn/bioconda/snakemake.svg?label=Bioconda&color=%23064e3b [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /conda/dn/bioconda/snakemake.svg?label=Bioconda&color=%23064e3b (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] WARNING: Could not fetch remote image: https://img.shields.io/pypi/pyversions/snakemake.svg?color=%23065f46 [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /pypi/pyversions/snakemake.svg?color=%23065f46 (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] WARNING: Could not fetch remote image: https://img.shields.io/pypi/v/snakemake.svg?color=%23047857 [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /pypi/v/snakemake.svg?color=%23047857 (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] WARNING: Could not fetch remote image: https://img.shields.io/github/actions/workflow/status/snakemake/snakemake/docker-publish.yml?label=docker%20container&branch=main&color=%23059669 [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /github/actions/workflow/status/snakemake/snakemake/docker-publish.yml?label=docker%20container&branch=main&color=%23059669 (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] WARNING: Could not fetch remote image: https://img.shields.io/github/actions/workflow/status/snakemake/snakemake/main.yml?label=tests&color=%2310b981 [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /github/actions/workflow/status/snakemake/snakemake/main.yml?label=tests&color=%2310b981 (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] WARNING: Could not fetch remote image: https://img.shields.io/badge/stack-overflow-orange.svg?color=%2334d399 [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/stack-overflow-orange.svg?color=%2334d399 (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] WARNING: Could not fetch remote image: https://img.shields.io/discord/753690260830945390?label=discord%20chat&color=%23a7f3d0 [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /discord/753690260830945390?label=discord%20chat&color=%23a7f3d0 (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] WARNING: Could not fetch remote image: https://img.shields.io/twitter/follow/johanneskoester.svg?style=social&label=Follow&color=%236ee7b7 [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /twitter/follow/johanneskoester.svg?style=social&label=Follow&color=%236ee7b7 (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] WARNING: Could not fetch remote image: https://img.shields.io/github/stars/snakemake/snakemake?style=social [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /github/stars/snakemake/snakemake?style=social (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] WARNING: Could not fetch remote image: https://img.shields.io/badge/snakemake-≥5.6.0-brightgreen.svg?style=flat [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/snakemake-%E2%89%A55.6.0-brightgreen.svg?style=flat (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] make: Leaving directory '/builddir/build/BUILD/snakemake-8.1.2/docs' /usr/bin/make -C _build/latex all-pdf make[1]: Entering directory '/builddir/build/BUILD/snakemake-8.1.2/docs/_build/latex' latexmk -pdf -dvi- -ps- 'Snakemake.tex' Rc files read: /etc/latexmkrc latexmkrc Latexmk: This is Latexmk, John Collins, 10 Jan. 2024. Version 4.82a. No existing .aux file, so I'll make a simple one, and require run of *latex. Latexmk: applying rule 'pdflatex'... 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(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1] [2] No file Snakemake.toc. [1] [2] [1] [2] Chapter 1. LaTeX Warning: Hyper reference `tutorial/tutorial:tutorial' on page 3 undefined on input line 143. LaTeX Warning: Hyper reference `project_info/faq:project-info-faq' on page 3 un defined on input line 143. LaTeX Warning: Hyper reference `snakefiles/best_practices:snakefiles-best-pract ices' on page 3 undefined on input line 147. [3] [4] Chapter 2. LaTeX Warning: Hyper reference `project_info/history:changelog' on page 5 undef ined on input line 156. LaTeX Warning: Hyper reference `project_info/faq:project-info-faq' on page 5 un defined on input line 160. LaTeX Warning: Hyper reference `project_info/contributing:project-info-contribu ting' on page 5 undefined on input line 176. [5] [6] Chapter 3. LaTeX Warning: Hyper reference `project_info/citations::doc' on page 7 undefine d on input line 191. [7] [8] Chapter 4. [9] LaTeX Warning: Hyper reference `snakefiles/deployment:integrated-package-manage ment' on page 10 undefined on input line 244. [10] LaTeX Warning: Hyper reference `snakefiles/rules:snakefiles-checkpoints' on pag e 11 undefined on input line 345. LaTeX Warning: Hyper reference `snakefiles/deployment:integrated-package-manage ment' on page 11 undefined on input line 349. LaTeX Warning: Hyper reference `snakefiles/deployment:apptainer' on page 11 und efined on input line 349. LaTeX Warning: Hyper reference `snakefiles/modularization:snakefiles-modules' o n page 11 undefined on input line 353. LaTeX Warning: Hyper reference `snakefiles/storage:storage-support' on page 11 undefined on input line 358. 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[190] [191] [192] [193] Underfull \hbox (badness 10000) in paragraph at lines 13533--13535 []\TU/FreeSerif(0)/m/n/10 provide temporary IPYTHONDIR for notebook execution i n order to avoid race conditions in [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] Underfull \hbox (badness 10000) in paragraph at lines 15997--16000 []\TU/FreeSerif(0)/m/n/10 Allow URL to local git repo with wrapper directive (\ TU/FreeMono(0)/m/n/10 git+file:///path/to/your/repo/ [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] Underfull \hbox (badness 10000) in paragraph at lines 17063--17069 []\TU/FreeSerif(0)/m/n/10 When submitting cluster jobs (either through [][]\TU/ FreeMono(0)/m/n/10 cluster \TU/FreeSerif(0)/m/n/10 or [][]\TU/FreeMono(0)/m/n/1 0 drmaa\TU/FreeSerif(0)/m/n/10 ), you can now use [229] [230] [231] No file Snakemake.ind. Package sphinx Warning: The package pict2e is required for rounded boxes. (sphinx) As it does not seem to be available on your system, (sphinx) options setting radii have all been ignored. Package sphinx Warning: The package ellipse is required for elliptical corners. (sphinx) As it does not seem to be available on your system, (sphinx) all non-straight corners have used circle arcs.. [232] (./Snakemake.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `Snakemake.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) Output written on Snakemake.pdf (236 pages). Transcript written on Snakemake.log. Latexmk: Getting log file 'Snakemake.log' Latexmk: Examining 'Snakemake.fls' Latexmk: Examining 'Snakemake.log' Latexmk: Index file 'Snakemake.idx' was written Latexmk: References changed. Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'Snakemake.pdf' Latexmk: applying rule 'makeindex Snakemake.idx'... Rule 'makeindex Snakemake.idx': Reasons for rerun Category 'other': Rerun of 'makeindex Snakemake.idx' forced or previously required ------------ Run number 1 of rule 'makeindex Snakemake.idx' ------------ ------------ Running 'internal xindy -L english -C utf8 -M sphinx.xdy -o "Snakemake.ind" "Snakemake.idx"' ------------ Latexmk: calling xindy( -L english -C utf8 -M sphinx.xdy -o "Snakemake.ind" "Snakemake.idx" ) Latexmk: applying rule 'pdflatex'... Rule 'pdflatex': Reasons for rerun Changed files or newly in use/created: Snakemake.aux Snakemake.ind Snakemake.out Snakemake.toc ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'xelatex -recorder "Snakemake.tex"' ------------ This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex) restricted \write18 enabled. entering extended mode (./Snakemake.tex LaTeX2e <2022-11-01> patch level 1 L3 programming layer <2023-02-22> (./sphinxmanual.cls Document Class: sphinxmanual 2019/12/01 v2.3.0 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2022/07/02 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty Package cmap Warning: pdftex not detected - exiting. ) (/usr/share/texlive/texmf-dist/tex/latex/fontspec/fontspec.sty (/usr/share/texlive/texmf-dist/tex/latex/l3packages/xparse/xparse.sty (/usr/share/texlive/texmf-dist/tex/latex/l3kernel/expl3.sty (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-xetex.def))) (/usr/share/texlive/texmf-dist/tex/latex/fontspec/fontspec-xetex.sty (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/fontspec/fontspec.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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[3] [4] Chapter 2. [5] [6] Chapter 3. [7] [8] Chapter 4. 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\TU/FreeMono(0)/m/n/10 code Underfull \hbox (badness 10000) in paragraph at lines 583--586 \TU/FreeSerif(0)/m/n/10 in- Overfull \hbox (81.52449pt too wide) in paragraph at lines 583--586 [][]\TU/FreeMono(0)/m/n/10 list[]code[]changes\TU/FreeSerif(0)/m/n/10 , Overfull \hbox (87.52449pt too wide) in paragraph at lines 583--586 [][]\TU/FreeMono(0)/m/n/10 list[]input[]changes\TU/FreeSerif(0)/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 583--586 \TU/FreeSerif(0)/m/n/10 or Overfull \hbox (91.02449pt too wide) in paragraph at lines 583--586 [][]\TU/FreeMono(0)/m/n/10 list[]params[]changes| Underfull \hbox (badness 10000) in paragraph at lines 587--589 []|\TU/FreeSerif(0)/m/n/10 bash- Underfull \hbox (badness 10000) in paragraph at lines 591--593 []|\TU/FreeSerif(0)/m/n/10 –bash- Underfull \hbox (badness 10000) in paragraph at lines 600--603 []|\TU/FreeSerif(0)/m/n/10 Unsup- Underfull \hbox (badness 10000) in paragraph at lines 608--610 []|\TU/FreeSerif(0)/m/n/10 –deploy- Underfull \hbox (badness 10000) in paragraph at lines 608--610 \TU/FreeSerif(0)/m/n/10 sources Underfull \hbox (badness 10000) in paragraph at lines 608--610 \TU/FreeSerif(0)/m/n/10 QUERY Underfull \hbox (badness 10000) in paragraph at lines 611--616 []|\TU/FreeSerif(0)/m/n/10 Deploy sources archive from Underfull \hbox (badness 10000) in paragraph at lines 629--632 []|\TU/FreeSerif(0)/m/n/10 Depre- Underfull \hbox (badness 10000) in paragraph at lines 629--632 \TU/FreeSerif(0)/m/n/10 cated: Underfull \hbox (badness 10000) in paragraph at lines 629--632 \TU/FreeSerif(0)/m/n/10 Drop Underfull \hbox (badness 10000) in paragraph at lines 629--632 \TU/FreeSerif(0)/m/n/10 it and Underfull \hbox (badness 10000) in paragraph at lines 629--632 \TU/FreeSerif(0)/m/n/10 don’t Underfull \hbox (badness 10000) in paragraph at lines 629--632 \TU/FreeSerif(0)/m/n/10 worry Underfull \hbox (badness 10000) in paragraph at lines 629--632 \TU/FreeSerif(0)/m/n/10 about Underfull \hbox (badness 10000) in paragraph at lines 650--653 []|\TU/FreeSerif(0)/m/n/10 Unsup- Underfull \hbox (badness 10000) in paragraph at lines 665--668 []|\TU/FreeSerif(0)/m/n/10 Unsup- Underfull \hbox (badness 10000) in paragraph at lines 673--675 []|\TU/FreeSerif(0)/m/n/10 –unneeded- Underfull \hbox (badness 10000) in paragraph at lines 673--675 \TU/FreeSerif(0)/m/n/10 temp-files Underfull \hbox (badness 10000) in paragraph at lines 673--675 \TU/FreeSerif(0)/m/n/10 FILE [FILE Underfull \hbox (badness 10000) in paragraph at lines 676--680 \TU/FreeSerif(0)/m/n/10 to storage and immediately Underfull \hbox (badness 10000) in paragraph at lines 676--680 \TU/FreeSerif(0)/m/n/10 deleted after job or group Underfull \hbox (badness 10000) in paragraph at lines 676--680 \TU/FreeSerif(0)/m/n/10 job completion. (default: Underfull \hbox (badness 10000) in paragraph at lines 689--691 []|\TU/FreeSerif(0)/m/n/10 –keep-storage- Underfull \hbox (badness 10000) in paragraph at lines 696--699 []|\TU/FreeSerif(0)/m/n/10 Re- Underfull \hbox (badness 10000) in paragraph at lines 700--702 []|\TU/FreeSerif(0)/m/n/10 –keep-target- Underfull \hbox (badness 10000) in paragraph at lines 707--709 []|\TU/FreeSerif(0)/m/n/10 –target-files- Underfull \hbox (badness 10000) in paragraph at lines 707--709 \TU/FreeSerif(0)/m/n/10 omit-workdir- Underfull \hbox (badness 10000) in paragraph at lines 714--717 []|\TU/FreeSerif(0)/m/n/10 Re- Underfull \hbox (badness 10000) in paragraph at lines 718--720 []|\TU/FreeSerif(0)/m/n/10 seconds- Underfull \hbox (badness 10000) in paragraph at lines 718--720 \TU/FreeSerif(0)/m/n/10 between- Underfull \hbox (badness 10000) in paragraph at lines 722--724 []|\TU/FreeSerif(0)/m/n/10 –seconds- Underfull \hbox (badness 10000) in paragraph at lines 722--724 \TU/FreeSerif(0)/m/n/10 between- Underfull \hbox (badness 10000) in paragraph at lines 722--724 \TU/FreeSerif(0)/m/n/10 status- Underfull \hbox (badness 10000) in paragraph at lines 722--724 \TU/FreeSerif(0)/m/n/10 checks SEC- Overfull \hbox (105.93674pt too wide) in paragraph at lines 722--724 \TU/FreeSerif(0)/m/n/10 ONDS_BETWEEN_STATUS_CHECKS| Underfull \hbox (badness 10000) in paragraph at lines 725--728 []|\TU/FreeSerif(0)/m/n/10 Number of seconds to wait Underfull \hbox (badness 10000) in paragraph at lines 734--736 []|\TU/FreeSerif(0)/m/n/10 –default- Underfull \hbox (badness 10000) in paragraph at lines 734--736 \TU/FreeSerif(0)/m/n/10 remote- Underfull \hbox (badness 10000) in paragraph at lines 734--736 \TU/FreeSerif(0)/m/n/10 provider Overfull \hbox (213.33673pt too wide) in paragraph at lines 734--736 \TU/FreeSerif(0)/m/n/10 {S3,GS,FTP,SFTP,S3Mocked,gfal,gridftp,iRODS,AzBlob,XRoo tD}| Underfull \hbox (badness 10000) in paragraph at lines 742--744 []|\TU/FreeSerif(0)/m/n/10 –default- Underfull \hbox (badness 10000) in paragraph at lines 742--744 \TU/FreeSerif(0)/m/n/10 storage- Underfull \hbox (badness 10000) in paragraph at lines 742--744 \TU/FreeSerif(0)/m/n/10 provider DE- Overfull \hbox (78.26674pt too wide) in paragraph at lines 742--744 \TU/FreeSerif(0)/m/n/10 FAULT_STORAGE_PROVIDER| Underfull \hbox (badness 10000) in paragraph at lines 745--752 \TU/FreeSerif(0)/m/n/10 output files that don’t yet Underfull \hbox (badness 10000) in paragraph at lines 745--752 [][]$[][][][][] [] [] [] [][][][][][][][][] [] [][][][][][] [] [][] [] Underfull \hbox (badness 10000) in paragraph at lines 745--752 [][][][][][][][][][][][][][][][][][][][][][][][][][]$[][] Underfull \hbox (badness 6493) in paragraph at lines 745--752 \TU/FreeSerif(0)/m/n/10 for available storage provider Overfull \hbox (8.55449pt too wide) in paragraph at lines 754--754 []|\TU/FreeSerif(0)/b/n/10 Renamed: Overfull \hbox (4.19449pt too wide) in paragraph at lines 754--758 \TU/FreeSerif(0)/m/n/10 See Overfull \hbox (11.83449pt too wide) in paragraph at lines 754--758 [][]$[][][][][] [] Underfull \hbox (badness 10000) in paragraph at lines 754--758 [] [] Overfull \hbox (36.71451pt too wide) in paragraph at lines 754--758 [][][][][][][][][] [] Overfull \hbox (17.68448pt too wide) in paragraph at lines 754--758 [][][][][][] [] Overfull \hbox (0.6745pt too wide) in paragraph at lines 754--758 [][] [] Overfull \hbox (94.82452pt too wide) in paragraph at lines 754--758 [][][][][][][][][][][][][][][][][][][][][][][][][][]$[][] Overfull \hbox (1.41449pt too wide) in paragraph at lines 754--758 \TU/FreeSerif(0)/m/n/10 for Overfull \hbox (11.49449pt too wide) in paragraph at lines 754--758 \TU/FreeSerif(0)/m/n/10 avail- Overfull \hbox (6.0945pt too wide) in paragraph at lines 754--758 \TU/FreeSerif(0)/m/n/10 able Overfull \hbox (8.0145pt too wide) in paragraph at lines 754--758 \TU/FreeSerif(0)/m/n/10 stor- Overfull \hbox (3.28448pt too wide) in paragraph at lines 754--758 \TU/FreeSerif(0)/m/n/10 age Overfull \hbox (22.8445pt too wide) in paragraph at lines 754--758 \TU/FreeSerif(0)/m/n/10 provider Overfull \hbox (5.63449pt too wide) in paragraph at lines 754--758 \TU/FreeSerif(0)/m/n/10 plu- Underfull \hbox (badness 10000) in paragraph at lines 754--758 \TU/FreeSerif(0)/m/n/10 g- Overfull \hbox (3.66449pt too wide) in paragraph at lines 754--758 \TU/FreeSerif(0)/m/n/10 ins. Underfull \hbox (badness 10000) in paragraph at lines 762--764 []|\TU/FreeSerif(0)/m/n/10 –default- Underfull \hbox (badness 10000) in paragraph at lines 762--764 \TU/FreeSerif(0)/m/n/10 remote- Underfull \hbox (badness 10000) in paragraph at lines 762--764 \TU/FreeSerif(0)/m/n/10 prefix DE- Overfull \hbox (58.22675pt too wide) in paragraph at lines 762--764 \TU/FreeSerif(0)/m/n/10 FAULT_REMOTE_PREFIX| Underfull \hbox (badness 10000) in paragraph at lines 769--771 []|\TU/FreeSerif(0)/m/n/10 –default- Underfull \hbox (badness 10000) in paragraph at lines 769--771 \TU/FreeSerif(0)/m/n/10 storage- Underfull \hbox (badness 10000) in paragraph at lines 769--771 \TU/FreeSerif(0)/m/n/10 prefix DE- Overfull \hbox (62.93675pt too wide) in paragraph at lines 769--771 \TU/FreeSerif(0)/m/n/10 FAULT_STORAGE_PREFIX| Underfull \hbox (badness 10000) in paragraph at lines 776--779 []|\TU/FreeSerif(0)/m/n/10 Re- Underfull \hbox (badness 10000) in paragraph at lines 780--782 []|\TU/FreeSerif(0)/m/n/10 –local-storage- Underfull \hbox (badness 10000) in paragraph at lines 780--782 \TU/FreeSerif(0)/m/n/10 prefix LO- Overfull \hbox (51.82675pt too wide) in paragraph at lines 780--782 \TU/FreeSerif(0)/m/n/10 CAL_STORAGE_PREFIX| Underfull \hbox (badness 10000) in paragraph at lines 812--814 []|\TU/FreeSerif(0)/m/n/10 –shared-fs- Underfull \hbox (badness 10000) in paragraph at lines 812--814 \TU/FreeSerif(0)/m/n/10 usage {input- Overfull \hbox (51.74675pt too wide) in paragraph at lines 812--814 \TU/FreeSerif(0)/m/n/10 output,persistence,software- Overfull \hbox (18.52675pt too wide) in paragraph at lines 812--814 \TU/FreeSerif(0)/m/n/10 deployment,source- Overfull \hbox (29.06674pt too wide) in paragraph at lines 812--814 \TU/FreeSerif(0)/m/n/10 cache,sources,storage- Underfull \hbox (badness 10000) in paragraph at lines 812--814 \TU/FreeSerif(0)/m/n/10 local- Underfull \hbox (badness 10000) in paragraph at lines 812--814 \TU/FreeSerif(0)/m/n/10 copies,none} Underfull \hbox (badness 10000) in paragraph at lines 812--814 \TU/FreeSerif(0)/m/n/10 [{input- Overfull \hbox (51.74675pt too wide) in paragraph at lines 812--814 \TU/FreeSerif(0)/m/n/10 output,persistence,software- Overfull \hbox (18.52675pt too wide) in paragraph at lines 812--814 \TU/FreeSerif(0)/m/n/10 deployment,source- Overfull \hbox (29.06674pt too wide) in paragraph at lines 812--814 \TU/FreeSerif(0)/m/n/10 cache,sources,storage- Underfull \hbox (badness 10000) in paragraph at lines 812--814 \TU/FreeSerif(0)/m/n/10 local- Underfull \hbox (badness 10000) in paragraph at lines 812--814 \TU/FreeSerif(0)/m/n/10 copies,none} Underfull \hbox (badness 10000) in paragraph at lines 815--835 []|\TU/FreeSerif(0)/m/n/10 Set assumptions on shared Underfull \hbox (badness 5578) in paragraph at lines 815--835 \TU/FreeSerif(0)/m/n/10 plugin sets this to a correct Underfull \hbox (badness 6001) in paragraph at lines 815--835 \TU/FreeSerif(0)/m/n/10 using ‘–default-storage-provider Overfull \hbox (113.30348pt too wide) in paragraph at lines 815--835 \TU/FreeSerif(0)/m/n/10 frozenset({, , , Underfull \hbox (badness 10000) in paragraph at lines 815--835 \TU/FreeSerif(0)/m/n/10 , , Overfull \hbox (19.02449pt too wide) in paragraph at lines 1060--1060 [][]\TU/FreeMono(0)/b/n/10 cluster Overfull \hbox (25.02449pt too wide) in paragraph at lines 1060--1060 [][]\TU/FreeMono(0)/b/n/10 executor Overfull \hbox (55.02449pt too wide) in paragraph at lines 1060--1060 \TU/FreeMono(0)/b/n/10 cluster[]generic Overfull \hbox (133.02449pt too wide) in paragraph at lines 1060--1060 [][]\TU/FreeMono(0)/b/n/10 cluster[]generic[]submit[]cmd Overfull \hbox (9.4545pt too wide) in paragraph at lines 1060--1062 \TU/FreeSerif(0)/m/n/10 Note Overfull \hbox (4.24449pt too wide) in paragraph at lines 1060--1062 \TU/FreeSerif(0)/m/n/10 you Overfull \hbox (15.4545pt too wide) in paragraph at lines 1060--1062 \TU/FreeSerif(0)/m/n/10 should Overfull \hbox (0.92448pt too wide) in paragraph at lines 1060--1062 \TU/FreeSerif(0)/m/n/10 in- Overfull \hbox (5.88449pt too wide) in paragraph at lines 1060--1062 \TU/FreeSerif(0)/m/n/10 stall Overfull \hbox (80.02449pt too wide) in paragraph at lines 1060--1062 \TU/FreeMono(0)/m/n/10 cluster[]generic Overfull \hbox (1.92448pt too wide) in paragraph at lines 1060--1062 \TU/FreeSerif(0)/m/n/10 us- Overfull \hbox (2.2645pt too wide) in paragraph at lines 1060--1062 \TU/FreeSerif(0)/m/n/10 ing Overfull \hbox (10.2945pt too wide) in paragraph at lines 1060--1062 \TU/FreeSerif(0)/m/n/10 com- Overfull \hbox (11.89449pt too wide) in paragraph at lines 1060--1062 \TU/FreeSerif(0)/m/n/10 mand Overfull \hbox (8.02449pt too wide) in paragraph at lines 1060--1062 \TU/FreeMono(0)/m/n/10 pip Overfull \hbox (8.02449pt too wide) in paragraph at lines 1060--1062 \TU/FreeMono(0)/m/n/10 in- Overfull \hbox (20.02449pt too wide) in paragraph at lines 1060--1062 \TU/FreeMono(0)/m/n/10 stall Overfull \hbox (194.02449pt too wide) in paragraph at lines 1060--1062 \TU/FreeMono(0)/m/n/10 snakemake[]executor[]cluster[]generic Underfull \hbox (badness 10000) in paragraph at lines 1081--1083 []|\TU/FreeSerif(0)/m/n/10 –cluster- Underfull \hbox (badness 10000) in paragraph at lines 1081--1083 \TU/FreeSerif(0)/m/n/10 generic- Underfull \hbox (badness 10000) in paragraph at lines 1081--1083 \TU/FreeSerif(0)/m/n/10 submit-cmd Underfull \hbox (badness 10000) in paragraph at lines 1084--1087 []|\TU/FreeSerif(0)/m/n/10 Command for submit- Underfull \hbox (badness 10000) in paragraph at lines 1084--1087 \TU/FreeSerif(0)/m/n/10 ting jobs (default: , , Underfull \hbox (badness 10000) in paragraph at lines 3448--3450 \TU/FreeSerif(0)/m/n/10 , , , Underfull \hbox (badness 10000) in paragraph at lines 3927--3929 \TU/FreeSerif(0)/m/n/10 , , [64] [65] [66] [67] [68] [69] Underfull \hbox (badness 10000) in paragraph at lines 4392--4395 []|\TU/FreeSerif(0)/m/n/10 Snakemake gets the status of panoptes. Underfull \hbox (badness 6859) in paragraph at lines 4392--4395 \TU/FreeSerif(0)/m/n/10 Snakemake continues to run if the status Underfull \hbox (badness 10000) in paragraph at lines 4409--4411 []|\TU/FreeMono(0)/m/n/10 / Overfull \hbox (9.78429pt too wide) in paragraph at lines 4409--4411 \TU/FreeMono(0)/m/n/10 update_workflow_status| [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] [91] [92] [93] [94] [95] [96] [97] Underfull \hbox (badness 5652) in paragraph at lines 6184--6188 \TU/FreeSerif(0)/m/n/10 Snakemake tracks the code that was used to create your files. In combination with [][]\TU/FreeMono(0)/m/n/10 summary \TU/FreeSerif(0)/ m/n/10 or [98] [99] [100] [101] [102] [103] [104] [105] Overfull \vbox (2.64099pt too high) detected at line 6753 [106] [107] [108] [109] [110] [111] [112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122] [123] [124] [125] [126] Underfull \hbox (badness 5878) in paragraph at lines 8045--8051 []\TU/FreeSerif(0)/m/n/10 First, we load a local configuration file. Next, we d efine the module \TU/FreeMono(0)/m/n/10 dna_seq \TU/FreeSerif(0)/m/n/10 to be l oaded from Overfull \vbox (1.03299pt too high) detected at line 8091 [127] Overfull \vbox (2.98596pt too high) detected at line 8140 [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] Underfull \hbox (badness 10000) in paragraph at lines 10274--10277 []\TU/FreeSerif(0)/m/n/10 Provide hyperlink targets, at least for the first two section levels. For this, use the format [159] [160] [161] [162] Missing character: There is no ⚠ (U+26A0) in font [FreeSansBold.otf]/OT:script= latn;language=dflt;! [163] Underfull \hbox (badness 10000) in paragraph at lines 10697--10699 \TU/FreeMono(0)/m/n/10 conda \TU/FreeSerif(0)/m/n/10 or [][]\TU/FreeMono(0)/m/n /10 software[]deployment[]method apptainer \TU/FreeSerif(0)/m/n/10 and [164] [165] [166] [167] [168] [169] [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185] [186] [187] [188] [189] Missing character: There is no ⚠ (U+26A0) in font [FreeSansBold.otf]/OT:script= latn;language=dflt;! [190] [191] [192] [193] Underfull \hbox (badness 10000) in paragraph at lines 13533--13535 []\TU/FreeSerif(0)/m/n/10 provide temporary IPYTHONDIR for notebook execution i n order to avoid race conditions in [194] [195] [196] [197] [198] [199] [200] [201] [202] [203] [204] [205] [206] [207] [208] [209] [210] [211] [212] [213] [214] [215] [216] [217] [218] Underfull \hbox (badness 10000) in paragraph at lines 15997--16000 []\TU/FreeSerif(0)/m/n/10 Allow URL to local git repo with wrapper directive (\ TU/FreeMono(0)/m/n/10 git+file:///path/to/your/repo/ [219] [220] [221] [222] [223] [224] [225] [226] [227] [228] Underfull \hbox (badness 10000) in paragraph at lines 17063--17069 []\TU/FreeSerif(0)/m/n/10 When submitting cluster jobs (either through [][]\TU/ FreeMono(0)/m/n/10 cluster \TU/FreeSerif(0)/m/n/10 or [][]\TU/FreeMono(0)/m/n/1 0 drmaa\TU/FreeSerif(0)/m/n/10 ), you can now use [229] [230] [231] (./Snakemake.ind) Package sphinx Warning: The package pict2e is required for rounded boxes. (sphinx) As it does not seem to be available on your system, (sphinx) options setting radii have all been ignored. Package sphinx Warning: The package ellipse is required for elliptical corners. (sphinx) As it does not seem to be available on your system, (sphinx) all non-straight corners have used circle arcs.. [232] (./Snakemake.aux) ) (see the transcript file for additional information) Output written on Snakemake.pdf (236 pages). Transcript written on Snakemake.log. Latexmk: Getting log file 'Snakemake.log' Latexmk: Examining 'Snakemake.fls' Latexmk: Examining 'Snakemake.log' Latexmk: Index file 'Snakemake.idx' was written Latexmk: Log file says output to 'Snakemake.pdf' Latexmk: Summary of warnings from last run of *latex: =====Latex reported missing or unavailable character(s). =====See log file for details. Latexmk: All targets () are up-to-date make[1]: Leaving directory '/builddir/build/BUILD/snakemake-8.1.2/docs/_build/latex' make: Entering directory '/builddir/build/BUILD/snakemake-8.1.2/docs' pdflatex finished; the PDF files are in _build/latex. make: Leaving directory '/builddir/build/BUILD/snakemake-8.1.2/docs' Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.olE4hz Latexmk: Missing input file 'Snakemake.toc' (or dependence on it) from following: No file Snakemake.toc. Latexmk: Missing input file 'Snakemake.ind' (or dependence on it) from following: No file Snakemake.ind. Latexmk: ====Undefined refs and citations with line #s in .tex file: Missing character: There is no ⚠ (U+26A0) in font [FreeSansBold.otf]/OT:script= Missing character: There is no ⚠ (U+26A0) in font [FreeSansBold.otf]/OT:script=latn;language=dflt;! Missing character: There is no ⚠ (U+26A0) in font [FreeSansBold.otf]/OT:script= Missing character: There is no ⚠ (U+26A0) in font [FreeSansBold.otf]/OT:script=latn;language=dflt;! + RPM_EC=0 ++ jobs -p + exit 0 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64 ++ dirname /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd snakemake-8.1.2 ++ xargs basename --multiple ++ ls /builddir/build/BUILD/snakemake-8.1.2/pyproject-wheeldir/snakemake-8.1.2-py3-none-any.whl ++ sed -E 's/([^-]+)-([^-]+)-.+\.whl/\1==\2/' + specifier=snakemake==8.1.2 + '[' -z snakemake==8.1.2 ']' + TMPDIR=/builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir + /usr/bin/python3 -m pip install --root /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64 --prefix /usr --no-deps --disable-pip-version-check --progress-bar off --verbose --ignore-installed --no-warn-script-location --no-index --no-cache-dir --find-links /builddir/build/BUILD/snakemake-8.1.2/pyproject-wheeldir snakemake==8.1.2 Using pip 23.3.1 from /usr/lib/python3.12/site-packages/pip (python 3.12) Looking in links: /builddir/build/BUILD/snakemake-8.1.2/pyproject-wheeldir Processing ./pyproject-wheeldir/snakemake-8.1.2-py3-none-any.whl Installing collected packages: snakemake Creating /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/bin changing mode of /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/bin/snakemake to 755 Successfully installed snakemake-8.1.2 + '[' -d /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/bin ']' + '[' -z sP ']' + shebang_flags=-kasP + /usr/bin/python3 -B /usr/lib/rpm/redhat/pathfix.py -pni /usr/bin/python3 -kasP /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/bin/snakemake /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/bin/snakemake: updating + rm -rfv /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/bin/__pycache__ + rm -f /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-ghost-distinfo + site_dirs=() + '[' -d /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib/python3.12/site-packages ']' + site_dirs+=("/usr/lib/python3.12/site-packages") + '[' /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib64/python3.12/site-packages '!=' /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib/python3.12/site-packages ']' + '[' -d /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib64/python3.12/site-packages ']' + for site_dir in ${site_dirs[@]} + for distinfo in /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64$site_dir/*.dist-info + echo '%ghost /usr/lib/python3.12/site-packages/snakemake-8.1.2.dist-info' + sed -i s/pip/rpm/ /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib/python3.12/site-packages/snakemake-8.1.2.dist-info/INSTALLER + PYTHONPATH=/usr/lib/rpm/redhat + /usr/bin/python3 -B /usr/lib/rpm/redhat/pyproject_preprocess_record.py --buildroot /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64 --record /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib/python3.12/site-packages/snakemake-8.1.2.dist-info/RECORD --output /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-record + rm -fv /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib/python3.12/site-packages/snakemake-8.1.2.dist-info/RECORD removed '/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib/python3.12/site-packages/snakemake-8.1.2.dist-info/RECORD' + rm -fv /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib/python3.12/site-packages/snakemake-8.1.2.dist-info/REQUESTED removed '/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib/python3.12/site-packages/snakemake-8.1.2.dist-info/REQUESTED' ++ wc -l /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-ghost-distinfo ++ cut -f1 '-d ' + lines=1 + '[' 1 -ne 1 ']' + RPM_PERCENTAGES_COUNT=2 + /usr/bin/python3 /usr/lib/rpm/redhat/pyproject_save_files.py --output-files /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-files --output-modules /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-modules --buildroot /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64 --sitelib /usr/lib/python3.12/site-packages --sitearch /usr/lib64/python3.12/site-packages --python-version 3.12 --pyproject-record /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-record --prefix /usr -l snakemake + install -d /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/man/man1 + PATH=/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/bin + PYTHONPATH=/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib/python3.12/site-packages + help2man --no-info '--name=Metapackage for snakemake: messaging extras' snakemake + install -t /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/nano -D -m 0644 -p misc/nano/syntax/snakemake.nanorc + install -d /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/vim/vimfiles + cp -vrp misc/vim/README.md misc/vim/ftdetect misc/vim/ftplugin misc/vim/syntax /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/vim/vimfiles 'misc/vim/README.md' -> '/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/vim/vimfiles/README.md' 'misc/vim/ftdetect' -> '/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/vim/vimfiles/ftdetect' 'misc/vim/ftdetect/snakemake.vim' -> '/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/vim/vimfiles/ftdetect/snakemake.vim' 'misc/vim/ftplugin' -> '/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/vim/vimfiles/ftplugin' 'misc/vim/ftplugin/snakemake' -> '/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/vim/vimfiles/ftplugin/snakemake' 'misc/vim/ftplugin/snakemake/folding.vim' -> '/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/vim/vimfiles/ftplugin/snakemake/folding.vim' 'misc/vim/ftplugin/snakemake/sections.vim' -> '/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/vim/vimfiles/ftplugin/snakemake/sections.vim' 'misc/vim/syntax' -> '/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/vim/vimfiles/syntax' 'misc/vim/syntax/snakemake.vim' -> '/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/vim/vimfiles/syntax/snakemake.vim' + find /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/vim/vimfiles -type f -name 'README.*' -print -delete /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/vim/vimfiles/README.md + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 8.1.2-2.fc40 --unique-debug-suffix -8.1.2-2.fc40.x86_64 --unique-debug-src-base snakemake-8.1.2-2.fc40.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/snakemake-8.1.2 find-debuginfo: starting Extracting debug info from 0 files Creating .debug symlinks for symlinks to ELF files find: ‘debug’: No such file or directory find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2 Bytecompiling .py files below /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib/python3.12 using python3.12 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.jnPzZ3 + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd snakemake-8.1.2 + '[' '!' -f /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-modules ']' + PATH=/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib/python3.12/site-packages + _PYTHONSITE=/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + /usr/bin/python3 -sP /usr/lib/rpm/redhat/import_all_modules.py -f /builddir/build/BUILD/snakemake-8.1.2-2.fc40.x86_64-pyproject-modules -e '*.tests*' -e snakemake.executors.flux Check import: snakemake Check import: snakemake.api Check import: snakemake.benchmark Check import: snakemake.caching Check import: snakemake.caching.hash Check import: snakemake.caching.local Check import: snakemake.caching.storage Check import: snakemake.checkpoints Check import: snakemake.cli Check import: snakemake.common Check import: snakemake.common.argparse Check import: snakemake.common.configfile Check import: snakemake.common.git Check import: snakemake.common.tbdstring Check import: snakemake.common.workdir_handler Check import: snakemake.cwl Check import: snakemake.dag Check import: snakemake.decorators Check import: snakemake.deployment Check import: snakemake.deployment.conda Check import: snakemake.deployment.containerize Check import: snakemake.deployment.env_modules Check import: snakemake.deployment.singularity Check import: snakemake.exceptions Check import: snakemake.executors Check import: snakemake.executors.dryrun Check import: snakemake.executors.google_lifesciences_helper Check import: snakemake.executors.local Check import: snakemake.executors.touch Check import: snakemake.gui Check import: snakemake.io Check import: snakemake.jobs Check import: snakemake.linting Check import: snakemake.linting.links Check import: snakemake.linting.rules Check import: snakemake.linting.snakefiles Check import: snakemake.logging Check import: snakemake.modules Check import: snakemake.notebook Check import: snakemake.output_index Check import: snakemake.parser Check import: snakemake.path_modifier Check import: snakemake.persistence Check import: snakemake.profiles Check import: snakemake.remote Check import: snakemake.remote.AzBlob Check import: snakemake.remote.EGA Check import: snakemake.remote.FTP Check import: snakemake.remote.GS Check import: snakemake.remote.HTTP Check import: snakemake.remote.NCBI Check import: snakemake.remote.S3 Check import: snakemake.remote.S3Mocked Check import: snakemake.remote.SFTP Check import: snakemake.remote.XRootD Check import: snakemake.remote.dropbox Check import: snakemake.remote.gfal Check import: snakemake.remote.gridftp Check import: snakemake.remote.iRODS Check import: snakemake.remote.webdav Check import: snakemake.remote.zenodo Check import: snakemake.report Check import: snakemake.report.data Check import: snakemake.report.data.categories Check import: snakemake.report.data.common Check import: snakemake.report.data.packages Check import: snakemake.report.data.results Check import: snakemake.report.data.rulegraph Check import: snakemake.report.data.rules Check import: snakemake.report.data.runtimes Check import: snakemake.report.data.timeline Check import: snakemake.report.rulegraph_spec Check import: snakemake.report.template Check import: snakemake.report.template.components Check import: snakemake.resources Check import: snakemake.ruleinfo Check import: snakemake.rules Check import: snakemake.scheduler Check import: snakemake.script Check import: snakemake.settings Check import: snakemake.shell Check import: snakemake.sourcecache Check import: snakemake.spawn_jobs Check import: snakemake.storage Check import: snakemake.target_jobs Check import: snakemake.template_rendering Check import: snakemake.template_rendering.jinja2 Check import: snakemake.template_rendering.yte Check import: snakemake.unit_tests Check import: snakemake.unit_tests.templates Check import: snakemake.utils Check import: snakemake.workflow Check import: snakemake.wrapper + ignore=' --ignore-glob=tests/test_google_lifesciences/*' + k='not test_deploy_sources' + ignore=' --ignore-glob=tests/test_google_lifesciences/* --ignore-glob=tests/test_conda_python_3_7_script/*' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + PATH=/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin + PYTHONPATH=/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib64/python3.12/site-packages:/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/lib/python3.12/site-packages + PYTHONDONTWRITEBYTECODE=1 + PYTEST_ADDOPTS=' --ignore=/builddir/build/BUILD/snakemake-8.1.2/.pyproject-builddir' + PYTEST_XDIST_AUTO_NUM_WORKERS=2 + /usr/bin/pytest -v -k 'not test_deploy_sources' '--ignore-glob=tests/test_google_lifesciences/*' '--ignore-glob=tests/test_conda_python_3_7_script/*' ============================= test session starts ============================== platform linux -- Python 3.12.1, pytest-7.4.3, pluggy-1.3.0 -- /usr/bin/python3 cachedir: .pytest_cache rootdir: /builddir/build/BUILD/snakemake-8.1.2 collecting ... collected 52 items / 1 deselected / 51 selected tests/test_executor_test_suite.py::TestWorkflows::test_simple_workflow PASSED [ 1%] tests/test_executor_test_suite.py::TestWorkflows::test_group_workflow PASSED [ 3%] tests/test_expand.py::test_simple_expand PASSED [ 5%] tests/test_expand.py::test_allow_missing PASSED [ 7%] tests/test_io.py::test_wildcard_regex PASSED [ 9%] tests/test_io.py::test_expand PASSED [ 11%] tests/test_linting.py::test_lint[tab_usage-positive] PASSED [ 13%] tests/test_linting.py::test_lint[tab_usage-negative] PASSED [ 15%] tests/test_linting.py::test_lint[singularity-positive] PASSED [ 17%] tests/test_linting.py::test_lint[singularity-negative] PASSED [ 19%] tests/test_linting.py::test_lint[path_add-positive] PASSED [ 21%] tests/test_linting.py::test_lint[path_add-negative] PASSED [ 23%] tests/test_linting.py::test_lint[params_prefix-positive] PASSED [ 25%] tests/test_linting.py::test_lint[params_prefix-negative] PASSED [ 27%] tests/test_linting.py::test_lint[not_used_params-positive] PASSED [ 29%] tests/test_linting.py::test_lint[not_used_params-negative] PASSED [ 31%] tests/test_linting.py::test_lint[mixed_func_and_rules-positive] PASSED [ 33%] tests/test_linting.py::test_lint[mixed_func_and_rules-negative] PASSED [ 35%] tests/test_linting.py::test_lint[missing_software_definition-positive] PASSED [ 37%] tests/test_linting.py::test_lint[missing_software_definition-negative] PASSED [ 39%] tests/test_linting.py::test_lint[long_run-positive] PASSED [ 41%] tests/test_linting.py::test_lint[long_run-negative] PASSED [ 43%] tests/test_linting.py::test_lint[log_directive-positive] PASSED [ 45%] tests/test_linting.py::test_lint[log_directive-negative] PASSED [ 47%] tests/test_linting.py::test_lint[iofile_by_index-positive] PASSED [ 49%] tests/test_linting.py::test_lint[iofile_by_index-negative] PASSED [ 50%] tests/test_linting.py::test_lint[envvars-positive] PASSED [ 52%] tests/test_linting.py::test_lint[envvars-negative] PASSED [ 54%] tests/test_linting.py::test_lint[absolute_paths-positive] PASSED [ 56%] tests/test_linting.py::test_lint[absolute_paths-negative] PASSED [ 58%] tests/test_persistence.py::TestCleanupContainers::test_one_unrequired_container_gets_removed PASSED [ 60%] tests/test_schema.py::test_config PASSED [ 62%] tests/test_schema.py::test_config_ref PASSED [ 64%] tests/test_schema.py::test_dataframe PASSED [ 66%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_with_shebang_and_second_manifest PASSED [ 68%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_not_at_start_with_shebang PASSED [ 70%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_not_at_start_without_shebang PASSED [ 72%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_with_empty_line_without_shebang PASSED [ 74%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_is_case_insensitive PASSED [ 76%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_spacing_has_no_impact PASSED [ 78%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_formatting_not_touched_even_if_wrong PASSED [ 80%] tests/test_script.py::TestRustScriptExtractManifest::test_single_line_manifest_spelt_wrong PASSED [ 82%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_with_shebang PASSED [ 84%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_without_shebang PASSED [ 86%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_spacing_around_language PASSED [ 88%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_has_non_cargo_block PASSED [ 90%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_missing_closing_fence PASSED [ 92%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_not_in_first_comment_block PASSED [ 94%] tests/test_script.py::TestRustScriptExtractManifest::test_code_block_manifest_with_outer_line_doc_comment PASSED [ 96%] tests/test_script.py::TestBashEncoder::test_named_list_one_named_one_str PASSED [ 98%] tests/test_script.py::TestBashEncoder::test_named_list_named_is_list PASSED [100%] =============================== warnings summary =============================== tests/test_executor_test_suite.py::TestWorkflows::test_simple_workflow :488: DeprecationWarning: Type google.protobuf.pyext._message.ScalarMapContainer uses PyType_Spec with a metaclass that has custom tp_new. This is deprecated and will no longer be allowed in Python 3.14. tests/test_executor_test_suite.py::TestWorkflows::test_simple_workflow :488: DeprecationWarning: Type google.protobuf.pyext._message.MessageMapContainer uses PyType_Spec with a metaclass that has custom tp_new. This is deprecated and will no longer be allowed in Python 3.14. tests/test_executor_test_suite.py::TestWorkflows::test_simple_workflow /usr/lib64/python3.12/site-packages/google/protobuf/internal/well_known_types.py:92: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC). _EPOCH_DATETIME = datetime.utcfromtimestamp(0) tests/test_schema.py: 12 warnings /builddir/build/BUILD/snakemake-8.1.2/snakemake/utils.py:52: DeprecationWarning: jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. A future release will remove RefResolver. Please file a feature request (on referencing) if you are missing an API for the kind of customization you need. from jsonschema import validators, RefResolver tests/test_schema.py::test_dataframe /usr/lib64/python3.12/site-packages/pandas/core/algorithms.py:522: DeprecationWarning: np.find_common_type is deprecated. Please use `np.result_type` or `np.promote_types`. See https://numpy.org/devdocs/release/1.25.0-notes.html and the docs for more information. (Deprecated NumPy 1.25) common = np.find_common_type([values.dtype, comps_array.dtype], []) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 51 passed, 1 deselected, 16 warnings in 81.71s (0:01:21) =========== + RPM_EC=0 ++ jobs -p + exit 0 Processing files: snakemake-8.1.2-2.fc40.noarch Provides: python3.12dist(snakemake) = 8.1.2 python3dist(snakemake) = 8.1.2 snakemake = 8.1.2-2.fc40 vim-snakemake = 8.1.2-2.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: (python3.12dist(conda-inject) < 2~~ with python3.12dist(conda-inject) >= 1.3.1) (python3.12dist(jinja2) < 4~~ with python3.12dist(jinja2) >= 3) (python3.12dist(pulp) < 2.9~~ with python3.12dist(pulp) >= 2.3.1) (python3.12dist(snakemake-interface-common) < 2~~ with python3.12dist(snakemake-interface-common) >= 1.15) (python3.12dist(snakemake-interface-executor-plugins) < 9~~ with python3.12dist(snakemake-interface-executor-plugins) >= 8.1.3) (python3.12dist(snakemake-interface-storage-plugins) < 4~~ with python3.12dist(snakemake-interface-storage-plugins) >= 3) (python3.12dist(yte) < 2~~ with python3.12dist(yte) >= 1.5.1) /usr/bin/python3 python(abi) = 3.12 python3.12dist(appdirs) python3.12dist(configargparse) python3.12dist(connection-pool) >= 0.0.3 python3.12dist(datrie) python3.12dist(docutils) python3.12dist(gitpython) python3.12dist(humanfriendly) python3.12dist(immutables) python3.12dist(jsonschema) python3.12dist(nbformat) python3.12dist(packaging) python3.12dist(psutil) python3.12dist(pyyaml) python3.12dist(requests) python3.12dist(reretry) python3.12dist(smart-open) >= 3 python3.12dist(stopit) python3.12dist(tabulate) python3.12dist(throttler) python3.12dist(toposort) >= 1.10 python3.12dist(wrapt) Obsoletes: snakemake+azure < 8.1.0-1 snakemake+google-cloud < 8.1.0-1 Processing files: snakemake-doc-8.1.2-2.fc40.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.5smkIr + umask 022 + cd /builddir/build/BUILD + cd snakemake-8.1.2 + DOCDIR=/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/doc/snakemake-doc + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/doc/snakemake-doc + cp -pr /builddir/build/BUILD/snakemake-8.1.2/CHANGELOG.md /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/doc/snakemake-doc + cp -pr /builddir/build/BUILD/snakemake-8.1.2/CODE_OF_CONDUCT.md /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/doc/snakemake-doc + cp -pr /builddir/build/BUILD/snakemake-8.1.2/README.md /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/doc/snakemake-doc + cp -pr /builddir/build/BUILD/snakemake-8.1.2/README-nano.md /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/doc/snakemake-doc + cp -pr /builddir/build/BUILD/snakemake-8.1.2/README-vim.md /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/doc/snakemake-doc + cp -pr /builddir/build/BUILD/snakemake-8.1.2/docs/_build/latex/Snakemake.pdf /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/doc/snakemake-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.Mv9bbK + umask 022 + cd /builddir/build/BUILD + cd snakemake-8.1.2 + LICENSEDIR=/builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/licenses/snakemake-doc + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/licenses/snakemake-doc + cp -pr /builddir/build/BUILD/snakemake-8.1.2/LICENSE.md /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64/usr/share/licenses/snakemake-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: snakemake-doc = 8.1.2-2.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: snakemake+reports-8.1.2-2.fc40.noarch Provides: python3.12dist(snakemake[reports]) = 8.1.2 python3dist(snakemake[reports]) = 8.1.2 snakemake+reports = 8.1.2-2.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: python(abi) = 3.12 python3.12dist(pygments) Processing files: snakemake+messaging-8.1.2-2.fc40.noarch Provides: python3.12dist(snakemake[messaging]) = 8.1.2 python3dist(snakemake[messaging]) = 8.1.2 snakemake+messaging = 8.1.2-2.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: python(abi) = 3.12 python3.12dist(slack-sdk) Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64 Wrote: /builddir/build/SRPMS/snakemake-8.1.2-2.fc40.src.rpm Wrote: /builddir/build/RPMS/snakemake-doc-8.1.2-2.fc40.noarch.rpm Wrote: /builddir/build/RPMS/snakemake+reports-8.1.2-2.fc40.noarch.rpm Wrote: /builddir/build/RPMS/snakemake+messaging-8.1.2-2.fc40.noarch.rpm Wrote: /builddir/build/RPMS/snakemake-8.1.2-2.fc40.noarch.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.hhcsTJ + umask 022 + cd /builddir/build/BUILD + cd snakemake-8.1.2 + /usr/bin/rm -rf /builddir/build/BUILDROOT/snakemake-8.1.2-2.fc40.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.RDkKLK + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/snakemake-8.1.2-SPECPARTS + rm -rf snakemake-8.1.2 snakemake-8.1.2.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild snakemake-8.1.2-2.fc40.src.rpm Finish: build phase for snakemake-8.1.2-2.fc40.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-39-x86_64-1705640458.173212/root/var/log/dnf.rpm.log /var/lib/mock/fedora-39-x86_64-1705640458.173212/root/var/log/dnf.librepo.log /var/lib/mock/fedora-39-x86_64-1705640458.173212/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/snakemake-8.1.2-2.fc40.src.rpm) Config(child) 3 minutes 30 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": "snakemake", "epoch": null, "version": "8.1.2", "release": "2.fc40", "arch": "noarch" }, { "name": "snakemake-doc", "epoch": null, "version": "8.1.2", "release": "2.fc40", "arch": "noarch" }, { "name": "snakemake", "epoch": null, "version": "8.1.2", "release": "2.fc40", "arch": "src" }, { "name": "snakemake+messaging", "epoch": null, "version": "8.1.2", "release": "2.fc40", "arch": "noarch" }, { "name": "snakemake+reports", "epoch": null, "version": "8.1.2", "release": "2.fc40", "arch": "noarch" } ] } RPMResults finished