Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c159' (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/8246339-fedora-41-x86_64 --chroot fedora-41-x86_64 Version: 1.1 PID: 6919 Logging PID: 6920 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 8246339, 'buildroot_pkgs': [], 'chroot': 'fedora-41-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'f9e83806c49ff5bd0288b26e742db65f309b9a45', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/thrnciar/pytest-8.3.1:pr:6/morphio', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'morphio', 'package_version': '3.4.0-1', 'project_dirname': 'pytest-8.3.1:pr:6', 'project_name': 'pytest-8.3.1', 'project_owner': 'thrnciar', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/thrnciar/pytest-8.3.1/fedora-41-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'thrnciar/pytest-8.3.1--https://src.fedoraproject.org/user/packit', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': None, 'submitter': 'https://src.fedoraproject.org/user/packit', 'tags': [], 'task_id': '8246339-fedora-41-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/thrnciar/pytest-8.3.1:pr:6/morphio /var/lib/copr-rpmbuild/workspace/workdir-hkmv63qg/morphio --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/thrnciar/pytest-8.3.1:pr:6/morphio', '/var/lib/copr-rpmbuild/workspace/workdir-hkmv63qg/morphio', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-hkmv63qg/morphio'... Running: git checkout f9e83806c49ff5bd0288b26e742db65f309b9a45 -- cmd: ['git', 'checkout', 'f9e83806c49ff5bd0288b26e742db65f309b9a45', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-hkmv63qg/morphio rc: 0 stdout: stderr: Note: switching to 'f9e83806c49ff5bd0288b26e742db65f309b9a45'. 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 f9e8380 automatic import of morphio Running: dist-git-client sources /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-hkmv63qg/morphio/morphio.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-hkmv63qg/morphio --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1731409031.927648 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.9 starting (python version = 3.12.1, NVR = mock-5.9-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-hkmv63qg/morphio/morphio.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-hkmv63qg/morphio --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1731409031.927648 -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-hkmv63qg/morphio/morphio.spec) Config(fedora-41-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.9 INFO: Mock Version: 5.9 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-41-x86_64-bootstrap-1731409031.927648/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:41 INFO: Pulling image: registry.fedoraproject.org/fedora:41 INFO: Copy content of container registry.fedoraproject.org/fedora:41 to /var/lib/mock/fedora-41-x86_64-bootstrap-1731409031.927648/root INFO: Checking that registry.fedoraproject.org/fedora:41 image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:41 with podman image mount INFO: image registry.fedoraproject.org/fedora:41 as /var/lib/containers/storage/overlay/7e5852cf95ae809dd6e7f959ffc81721eaa8c6008a1c6d7b2db4c7341e265462/merged INFO: umounting image registry.fedoraproject.org/fedora:41 (/var/lib/containers/storage/overlay/7e5852cf95ae809dd6e7f959ffc81721eaa8c6008a1c6d7b2db4c7341e265462/merged) with podman image umount INFO: Package manager dnf5 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True 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-41-x86_64-1731409031.927648/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 dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.20.0-1.fc41.x86_64 rpm-sequoia-1.7.0-2.fc41.x86_64 dnf5-5.2.6.2-1.fc41.x86_64 dnf5-plugins-5.2.6.2-1.fc41.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: updates 100% | 3.0 MiB/s | 4.2 MiB | 00m01s fedora 100% | 1.9 MiB/s | 35.4 MiB | 00m18s Copr repository 100% | 12.8 MiB/s | 1.7 MiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.2.32-1.fc41 fedora 8.2 MiB bzip2 x86_64 1.0.8-19.fc41 fedora 95.7 KiB coreutils x86_64 9.5-10.fc41 fedora 5.6 MiB cpio x86_64 2.15-2.fc41 fedora 1.1 MiB diffutils x86_64 3.10-8.fc41 fedora 1.6 MiB fedora-release-common noarch 41-27 updates 19.6 KiB findutils x86_64 1:4.10.0-4.fc41 fedora 1.8 MiB gawk x86_64 5.3.0-4.fc41 fedora 1.7 MiB glibc-minimal-langpack x86_64 2.40-9.fc41 updates 0.0 B grep x86_64 3.11-9.fc41 fedora 1.0 MiB gzip x86_64 1.13-2.fc41 fedora 389.0 KiB info x86_64 7.1-3.fc41 fedora 361.8 KiB patch x86_64 2.7.6-25.fc41 fedora 266.7 KiB redhat-rpm-config noarch 293-1.fc41 fedora 183.5 KiB rpm-build x86_64 4.20.0-1.fc41 fedora 194.3 KiB sed x86_64 4.9-3.fc41 fedora 861.5 KiB shadow-utils x86_64 2:4.15.1-12.fc41 fedora 4.1 MiB tar x86_64 2:1.35-4.fc41 fedora 2.9 MiB unzip x86_64 6.0-64.fc41 fedora 386.8 KiB util-linux x86_64 2.40.2-4.fc41 fedora 3.7 MiB which x86_64 2.21-42.fc41 fedora 80.2 KiB xz x86_64 1:5.6.2-2.fc41 fedora 1.2 MiB Installing dependencies: add-determinism x86_64 0.3.6-1.fc41 fedora 2.2 MiB alternatives x86_64 1.30-1.fc41 fedora 66.3 KiB ansible-srpm-macros noarch 1-16.fc41 fedora 35.7 KiB audit-libs x86_64 4.0.2-1.fc41 fedora 331.3 KiB authselect x86_64 1.5.0-8.fc41 fedora 157.6 KiB authselect-libs x86_64 1.5.0-8.fc41 fedora 822.2 KiB basesystem noarch 11-21.fc41 fedora 0.0 B binutils x86_64 2.43.1-2.fc41 fedora 27.5 MiB build-reproducibility-srpm-macros noarch 0.3.6-1.fc41 fedora 735.0 B bzip2-libs x86_64 1.0.8-19.fc41 fedora 80.7 KiB ca-certificates noarch 2024.2.69_v8.0.401-1.0.fc41 fedora 2.4 MiB coreutils-common x86_64 9.5-10.fc41 fedora 11.2 MiB cracklib x86_64 2.9.11-6.fc41 fedora 238.9 KiB crypto-policies noarch 20241029-1.git8baf557.fc41 updates 136.9 KiB curl x86_64 8.9.1-2.fc41 fedora 796.2 KiB cyrus-sasl-lib x86_64 2.1.28-27.fc41 fedora 2.3 MiB debugedit x86_64 5.1-1.fc41 updates 199.8 KiB dwz x86_64 0.15-8.fc41 fedora 298.9 KiB ed x86_64 1.20.2-2.fc41 fedora 146.9 KiB efi-srpm-macros noarch 5-12.fc41 fedora 40.1 KiB elfutils x86_64 0.192-5.fc41 updates 2.7 MiB elfutils-debuginfod-client x86_64 0.192-5.fc41 updates 84.2 KiB elfutils-default-yama-scope noarch 0.192-5.fc41 updates 1.8 KiB elfutils-libelf x86_64 0.192-5.fc41 updates 1.2 MiB elfutils-libs x86_64 0.192-5.fc41 updates 666.3 KiB fedora-gpg-keys noarch 41-1 fedora 126.4 KiB fedora-release noarch 41-27 updates 0.0 B fedora-release-identity-basic noarch 41-27 updates 682.0 B fedora-repos noarch 41-1 fedora 4.9 KiB file x86_64 5.45-7.fc41 fedora 103.5 KiB file-libs x86_64 5.45-7.fc41 fedora 9.9 MiB filesystem x86_64 3.18-23.fc41 fedora 106.0 B fonts-srpm-macros noarch 1:2.0.5-17.fc41 fedora 55.8 KiB forge-srpm-macros noarch 0.4.0-1.fc41 copr_base 38.9 KiB fpc-srpm-macros noarch 1.3-13.fc41 fedora 144.0 B gdb-minimal x86_64 15.2-2.fc41 updates 13.0 MiB gdbm x86_64 1:1.23-7.fc41 fedora 460.9 KiB gdbm-libs x86_64 1:1.23-7.fc41 fedora 121.9 KiB ghc-srpm-macros noarch 1.9.1-2.fc41 fedora 747.0 B glibc x86_64 2.40-9.fc41 updates 6.7 MiB glibc-common x86_64 2.40-9.fc41 updates 1.0 MiB glibc-gconv-extra x86_64 2.40-9.fc41 updates 8.0 MiB gmp x86_64 1:6.3.0-2.fc41 fedora 811.4 KiB gnat-srpm-macros noarch 6-6.fc41 fedora 1.0 KiB go-srpm-macros noarch 3.6.0-3.fc41 fedora 60.8 KiB jansson x86_64 2.13.1-10.fc41 fedora 88.3 KiB json-c x86_64 0.17-4.fc41 fedora 82.4 KiB kernel-srpm-macros noarch 1.0-24.fc41 fedora 1.9 KiB keyutils-libs x86_64 1.6.3-4.fc41 fedora 54.4 KiB krb5-libs x86_64 1.21.3-3.fc41 updates 2.3 MiB libacl x86_64 2.3.2-2.fc41 fedora 40.0 KiB libarchive x86_64 3.7.4-4.fc41 updates 926.6 KiB libattr x86_64 2.5.2-4.fc41 fedora 28.5 KiB libblkid x86_64 2.40.2-4.fc41 fedora 258.5 KiB libbrotli x86_64 1.1.0-5.fc41 fedora 837.6 KiB libcap x86_64 2.70-4.fc41 fedora 220.2 KiB libcap-ng x86_64 0.8.5-3.fc41 fedora 69.2 KiB libcom_err x86_64 1.47.1-6.fc41 fedora 67.2 KiB libcurl x86_64 8.9.1-2.fc41 fedora 818.1 KiB libeconf x86_64 0.6.2-3.fc41 fedora 58.0 KiB libevent x86_64 2.1.12-14.fc41 fedora 895.7 KiB libfdisk x86_64 2.40.2-4.fc41 fedora 362.9 KiB libffi x86_64 3.4.6-3.fc41 fedora 86.4 KiB libgcc x86_64 14.2.1-3.fc41 fedora 274.6 KiB libgomp x86_64 14.2.1-3.fc41 fedora 523.5 KiB libidn2 x86_64 2.3.7-2.fc41 fedora 329.1 KiB libmount x86_64 2.40.2-4.fc41 fedora 351.8 KiB libnghttp2 x86_64 1.62.1-2.fc41 fedora 166.1 KiB libnsl2 x86_64 2.0.1-2.fc41 fedora 57.9 KiB libpkgconf x86_64 2.3.0-1.fc41 fedora 78.2 KiB libpsl x86_64 0.21.5-4.fc41 fedora 80.5 KiB libpwquality x86_64 1.4.5-11.fc41 fedora 417.8 KiB libselinux x86_64 3.7-5.fc41 fedora 181.0 KiB libsemanage x86_64 3.7-2.fc41 fedora 293.5 KiB libsepol x86_64 3.7-2.fc41 fedora 817.8 KiB libsmartcols x86_64 2.40.2-4.fc41 fedora 180.4 KiB libssh x86_64 0.10.6-8.fc41 fedora 513.3 KiB libssh-config noarch 0.10.6-8.fc41 fedora 277.0 B libstdc++ x86_64 14.2.1-3.fc41 fedora 2.8 MiB libtasn1 x86_64 4.19.0-9.fc41 fedora 175.7 KiB libtirpc x86_64 1.3.6-0.fc41 updates 202.7 KiB libtool-ltdl x86_64 2.4.7-12.fc41 fedora 66.2 KiB libunistring x86_64 1.1-8.fc41 fedora 1.7 MiB libutempter x86_64 1.2.1-15.fc41 fedora 57.7 KiB libuuid x86_64 2.40.2-4.fc41 fedora 37.5 KiB libverto x86_64 0.3.2-9.fc41 fedora 29.5 KiB libxcrypt x86_64 4.4.36-10.fc41 updates 271.4 KiB libxml2 x86_64 2.12.8-2.fc41 fedora 1.7 MiB libzstd x86_64 1.5.6-2.fc41 fedora 795.9 KiB lua-libs x86_64 5.4.6-6.fc41 fedora 285.0 KiB lua-srpm-macros noarch 1-14.fc41 fedora 1.3 KiB lz4-libs x86_64 1.10.0-1.fc41 fedora 145.5 KiB mpfr x86_64 4.2.1-5.fc41 fedora 832.1 KiB ncurses-base noarch 6.5-2.20240629.fc41 fedora 326.3 KiB ncurses-libs x86_64 6.5-2.20240629.fc41 fedora 975.2 KiB ocaml-srpm-macros noarch 10-3.fc41 fedora 1.9 KiB openblas-srpm-macros noarch 2-18.fc41 fedora 112.0 B openldap x86_64 2.6.8-5.fc41 fedora 644.2 KiB openssl-libs x86_64 1:3.2.2-9.fc41 fedora 7.8 MiB p11-kit x86_64 0.25.5-3.fc41 fedora 2.2 MiB p11-kit-trust x86_64 0.25.5-3.fc41 fedora 391.4 KiB package-notes-srpm-macros noarch 0.5-12.fc41 fedora 1.6 KiB pam x86_64 1.6.1-6.fc41 updates 1.8 MiB pam-libs x86_64 1.6.1-6.fc41 updates 139.0 KiB pcre2 x86_64 10.44-1.fc41.1 fedora 653.5 KiB pcre2-syntax noarch 10.44-1.fc41.1 fedora 251.6 KiB perl-srpm-macros noarch 1-56.fc41 fedora 861.0 B pkgconf x86_64 2.3.0-1.fc41 fedora 88.6 KiB pkgconf-m4 noarch 2.3.0-1.fc41 fedora 14.4 KiB pkgconf-pkg-config x86_64 2.3.0-1.fc41 fedora 989.0 B popt x86_64 1.19-7.fc41 fedora 136.9 KiB publicsuffix-list-dafsa noarch 20240107-4.fc41 fedora 67.5 KiB pyproject-srpm-macros noarch 1.16.1-1.fc41 copr_base 1.9 KiB python-srpm-macros noarch 3.13-3.fc41 fedora 51.0 KiB qt5-srpm-macros noarch 5.15.15-1.fc41 fedora 500.0 B qt6-srpm-macros noarch 6.8.0-1.fc41 updates 456.0 B readline x86_64 8.2-10.fc41 fedora 493.2 KiB rpm x86_64 4.20.0-1.fc41 fedora 3.1 MiB rpm-build-libs x86_64 4.20.0-1.fc41 fedora 206.7 KiB rpm-libs x86_64 4.20.0-1.fc41 fedora 725.9 KiB rpm-sequoia x86_64 1.7.0-2.fc41 fedora 2.4 MiB rust-srpm-macros noarch 26.3-3.fc41 copr_base 4.8 KiB setup noarch 2.15.0-5.fc41 fedora 720.7 KiB sqlite-libs x86_64 3.46.1-1.fc41 fedora 1.4 MiB systemd-libs x86_64 257~rc1-2.fc41 copr_base 2.3 MiB util-linux-core x86_64 2.40.2-4.fc41 fedora 1.5 MiB xxhash-libs x86_64 0.8.2-4.fc41 fedora 88.4 KiB xz-libs x86_64 1:5.6.2-2.fc41 fedora 214.4 KiB zig-srpm-macros noarch 1-3.fc41 fedora 1.1 KiB zip x86_64 3.0-41.fc41 fedora 703.2 KiB zlib-ng-compat x86_64 2.1.7-3.fc41 fedora 134.0 KiB zstd x86_64 1.5.6-2.fc41 fedora 1.7 MiB Installing groups: Buildsystem building group Transaction Summary: Installing: 154 packages Total size of inbound packages is 53 MiB. Need to download 53 MiB. After this operation, 181 MiB extra will be used (install 181 MiB, remove 0 B). [ 1/154] bzip2-0:1.0.8-19.fc41.x86_64 100% | 413.6 KiB/s | 52.5 KiB | 00m00s [ 2/154] cpio-0:2.15-2.fc41.x86_64 100% | 3.4 MiB/s | 291.8 KiB | 00m00s [ 3/154] coreutils-0:9.5-10.fc41.x86_6 100% | 5.0 MiB/s | 1.1 MiB | 00m00s [ 4/154] bash-0:5.2.32-1.fc41.x86_64 100% | 7.2 MiB/s | 1.8 MiB | 00m00s [ 5/154] findutils-1:4.10.0-4.fc41.x86 100% | 17.3 MiB/s | 548.5 KiB | 00m00s [ 6/154] diffutils-0:3.10-8.fc41.x86_6 100% | 8.1 MiB/s | 405.4 KiB | 00m00s [ 7/154] grep-0:3.11-9.fc41.x86_64 100% | 11.3 MiB/s | 299.7 KiB | 00m00s [ 8/154] gzip-0:1.13-2.fc41.x86_64 100% | 6.6 MiB/s | 170.2 KiB | 00m00s [ 9/154] info-0:7.1-3.fc41.x86_64 100% | 6.6 MiB/s | 182.5 KiB | 00m00s [ 10/154] patch-0:2.7.6-25.fc41.x86_64 100% | 5.3 MiB/s | 131.0 KiB | 00m00s [ 11/154] redhat-rpm-config-0:293-1.fc4 100% | 3.3 MiB/s | 82.0 KiB | 00m00s [ 12/154] rpm-build-0:4.20.0-1.fc41.x86 100% | 3.2 MiB/s | 82.8 KiB | 00m00s [ 13/154] sed-0:4.9-3.fc41.x86_64 100% | 11.9 MiB/s | 317.7 KiB | 00m00s [ 14/154] 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-------------------------------------------------------------------------------- [154/154] Total 100% | 27.2 MiB/s | 53.3 MiB | 00m02s Running transaction Importing PGP key 0xE99D6AD1: UserID : "Fedora (41) " Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary The key was successfully imported. 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authselect-0:1.5.0 100% | 39.5 MiB/s | 161.9 KiB | 00m00s [155/156] Installing which-0:2.21-42.fc 100% | 40.2 MiB/s | 82.4 KiB | 00m00s [156/156] Installing info-0:7.1-3.fc41. 100% | 278.6 KiB/s | 362.2 KiB | 00m01s Warning: skipped PGP checks for 4 packages from repository: copr_base Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.3.6-1.fc41.x86_64 alternatives-1.30-1.fc41.x86_64 ansible-srpm-macros-1-16.fc41.noarch audit-libs-4.0.2-1.fc41.x86_64 authselect-1.5.0-8.fc41.x86_64 authselect-libs-1.5.0-8.fc41.x86_64 basesystem-11-21.fc41.noarch bash-5.2.32-1.fc41.x86_64 binutils-2.43.1-2.fc41.x86_64 build-reproducibility-srpm-macros-0.3.6-1.fc41.noarch bzip2-1.0.8-19.fc41.x86_64 bzip2-libs-1.0.8-19.fc41.x86_64 ca-certificates-2024.2.69_v8.0.401-1.0.fc41.noarch coreutils-9.5-10.fc41.x86_64 coreutils-common-9.5-10.fc41.x86_64 cpio-2.15-2.fc41.x86_64 cracklib-2.9.11-6.fc41.x86_64 crypto-policies-20241029-1.git8baf557.fc41.noarch curl-8.9.1-2.fc41.x86_64 cyrus-sasl-lib-2.1.28-27.fc41.x86_64 debugedit-5.1-1.fc41.x86_64 diffutils-3.10-8.fc41.x86_64 dwz-0.15-8.fc41.x86_64 ed-1.20.2-2.fc41.x86_64 efi-srpm-macros-5-12.fc41.noarch elfutils-0.192-5.fc41.x86_64 elfutils-debuginfod-client-0.192-5.fc41.x86_64 elfutils-default-yama-scope-0.192-5.fc41.noarch elfutils-libelf-0.192-5.fc41.x86_64 elfutils-libs-0.192-5.fc41.x86_64 fedora-gpg-keys-41-1.noarch fedora-release-41-27.noarch fedora-release-common-41-27.noarch fedora-release-identity-basic-41-27.noarch fedora-repos-41-1.noarch file-5.45-7.fc41.x86_64 file-libs-5.45-7.fc41.x86_64 filesystem-3.18-23.fc41.x86_64 findutils-4.10.0-4.fc41.x86_64 fonts-srpm-macros-2.0.5-17.fc41.noarch forge-srpm-macros-0.4.0-1.fc41.noarch fpc-srpm-macros-1.3-13.fc41.noarch gawk-5.3.0-4.fc41.x86_64 gdb-minimal-15.2-2.fc41.x86_64 gdbm-1.23-7.fc41.x86_64 gdbm-libs-1.23-7.fc41.x86_64 ghc-srpm-macros-1.9.1-2.fc41.noarch glibc-2.40-9.fc41.x86_64 glibc-common-2.40-9.fc41.x86_64 glibc-gconv-extra-2.40-9.fc41.x86_64 glibc-minimal-langpack-2.40-9.fc41.x86_64 gmp-6.3.0-2.fc41.x86_64 gnat-srpm-macros-6-6.fc41.noarch go-srpm-macros-3.6.0-3.fc41.noarch gpg-pubkey-e99d6ad1-64d2612c grep-3.11-9.fc41.x86_64 gzip-1.13-2.fc41.x86_64 info-7.1-3.fc41.x86_64 jansson-2.13.1-10.fc41.x86_64 json-c-0.17-4.fc41.x86_64 kernel-srpm-macros-1.0-24.fc41.noarch keyutils-libs-1.6.3-4.fc41.x86_64 krb5-libs-1.21.3-3.fc41.x86_64 libacl-2.3.2-2.fc41.x86_64 libarchive-3.7.4-4.fc41.x86_64 libattr-2.5.2-4.fc41.x86_64 libblkid-2.40.2-4.fc41.x86_64 libbrotli-1.1.0-5.fc41.x86_64 libcap-2.70-4.fc41.x86_64 libcap-ng-0.8.5-3.fc41.x86_64 libcom_err-1.47.1-6.fc41.x86_64 libcurl-8.9.1-2.fc41.x86_64 libeconf-0.6.2-3.fc41.x86_64 libevent-2.1.12-14.fc41.x86_64 libfdisk-2.40.2-4.fc41.x86_64 libffi-3.4.6-3.fc41.x86_64 libgcc-14.2.1-3.fc41.x86_64 libgomp-14.2.1-3.fc41.x86_64 libidn2-2.3.7-2.fc41.x86_64 libmount-2.40.2-4.fc41.x86_64 libnghttp2-1.62.1-2.fc41.x86_64 libnsl2-2.0.1-2.fc41.x86_64 libpkgconf-2.3.0-1.fc41.x86_64 libpsl-0.21.5-4.fc41.x86_64 libpwquality-1.4.5-11.fc41.x86_64 libselinux-3.7-5.fc41.x86_64 libsemanage-3.7-2.fc41.x86_64 libsepol-3.7-2.fc41.x86_64 libsmartcols-2.40.2-4.fc41.x86_64 libssh-0.10.6-8.fc41.x86_64 libssh-config-0.10.6-8.fc41.noarch libstdc++-14.2.1-3.fc41.x86_64 libtasn1-4.19.0-9.fc41.x86_64 libtirpc-1.3.6-0.fc41.x86_64 libtool-ltdl-2.4.7-12.fc41.x86_64 libunistring-1.1-8.fc41.x86_64 libutempter-1.2.1-15.fc41.x86_64 libuuid-2.40.2-4.fc41.x86_64 libverto-0.3.2-9.fc41.x86_64 libxcrypt-4.4.36-10.fc41.x86_64 libxml2-2.12.8-2.fc41.x86_64 libzstd-1.5.6-2.fc41.x86_64 lua-libs-5.4.6-6.fc41.x86_64 lua-srpm-macros-1-14.fc41.noarch lz4-libs-1.10.0-1.fc41.x86_64 mpfr-4.2.1-5.fc41.x86_64 ncurses-base-6.5-2.20240629.fc41.noarch ncurses-libs-6.5-2.20240629.fc41.x86_64 ocaml-srpm-macros-10-3.fc41.noarch openblas-srpm-macros-2-18.fc41.noarch openldap-2.6.8-5.fc41.x86_64 openssl-libs-3.2.2-9.fc41.x86_64 p11-kit-0.25.5-3.fc41.x86_64 p11-kit-trust-0.25.5-3.fc41.x86_64 package-notes-srpm-macros-0.5-12.fc41.noarch pam-1.6.1-6.fc41.x86_64 pam-libs-1.6.1-6.fc41.x86_64 patch-2.7.6-25.fc41.x86_64 pcre2-10.44-1.fc41.1.x86_64 pcre2-syntax-10.44-1.fc41.1.noarch perl-srpm-macros-1-56.fc41.noarch pkgconf-2.3.0-1.fc41.x86_64 pkgconf-m4-2.3.0-1.fc41.noarch pkgconf-pkg-config-2.3.0-1.fc41.x86_64 popt-1.19-7.fc41.x86_64 publicsuffix-list-dafsa-20240107-4.fc41.noarch pyproject-srpm-macros-1.16.1-1.fc41.noarch python-srpm-macros-3.13-3.fc41.noarch qt5-srpm-macros-5.15.15-1.fc41.noarch qt6-srpm-macros-6.8.0-1.fc41.noarch readline-8.2-10.fc41.x86_64 redhat-rpm-config-293-1.fc41.noarch rpm-4.20.0-1.fc41.x86_64 rpm-build-4.20.0-1.fc41.x86_64 rpm-build-libs-4.20.0-1.fc41.x86_64 rpm-libs-4.20.0-1.fc41.x86_64 rpm-sequoia-1.7.0-2.fc41.x86_64 rust-srpm-macros-26.3-3.fc41.noarch sed-4.9-3.fc41.x86_64 setup-2.15.0-5.fc41.noarch shadow-utils-4.15.1-12.fc41.x86_64 sqlite-libs-3.46.1-1.fc41.x86_64 systemd-libs-257~rc1-2.fc41.x86_64 tar-1.35-4.fc41.x86_64 unzip-6.0-64.fc41.x86_64 util-linux-2.40.2-4.fc41.x86_64 util-linux-core-2.40.2-4.fc41.x86_64 which-2.21-42.fc41.x86_64 xxhash-libs-0.8.2-4.fc41.x86_64 xz-5.6.2-2.fc41.x86_64 xz-libs-5.6.2-2.fc41.x86_64 zig-srpm-macros-1-3.fc41.noarch zip-3.0-41.fc41.x86_64 zlib-ng-compat-2.1.7-3.fc41.x86_64 zstd-1.5.6-2.fc41.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1731369600 Wrote: /builddir/build/SRPMS/morphio-3.4.0-1.fc41.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-41-x86_64-1731409031.927648/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-hkmv63qg/morphio/morphio.spec) Config(child) 0 minutes 48 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/morphio-3.4.0-1.fc41.src.rpm) Config(fedora-41-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-41-x86_64-bootstrap-1731409031.927648/root. INFO: reusing tmpfs at /var/lib/mock/fedora-41-x86_64-bootstrap-1731409031.927648/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-41-x86_64-1731409031.927648/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-4.20.0-1.fc41.x86_64 rpm-sequoia-1.7.0-2.fc41.x86_64 dnf5-5.2.6.2-1.fc41.x86_64 dnf5-plugins-5.2.6.2-1.fc41.x86_64 Finish: chroot init Start: build phase for morphio-3.4.0-1.fc41.src.rpm Start: build setup for morphio-3.4.0-1.fc41.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1731369600 Wrote: /builddir/build/SRPMS/morphio-3.4.0-1.fc41.src.rpm Updating and loading repositories: updates 100% | 1.0 MiB/s | 29.9 KiB | 00m00s fedora 100% | 1.0 MiB/s | 26.8 KiB | 00m00s Copr repository 100% | 51.1 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: boost-devel x86_64 1.83.0-8.fc41 fedora 143.0 MiB catch2-devel x86_64 2.13.10-5.fc41 fedora 952.8 KiB cmake x86_64 3.30.5-1.fc41 updates 32.5 MiB gcc-c++ x86_64 14.2.1-3.fc41 fedora 38.2 MiB gsl-lite-devel x86_64 0.41.0-5.fc41 fedora 308.1 KiB gulrak-filesystem-devel x86_64 1.5.14-8.fc41 fedora 272.2 KiB hdf5-devel x86_64 1.12.1-20.fc41 fedora 3.9 MiB highfive-devel x86_64 2.10.0-1.fc41 fedora 377.0 KiB lcov noarch 2.0-4.fc41 fedora 930.9 KiB lexertl14-devel x86_64 1:0.1.0^20240506gitbca1359-2.fc41 fedora 573.7 KiB ninja-build x86_64 1.12.1-3.fc41 fedora 432.6 KiB pybind11-devel x86_64 2.13.6-1.fc41 copr_base 847.8 KiB python3-devel x86_64 3.13.0-1.fc41 fedora 1.8 MiB python3-h5py x86_64 3.12.1-3.fc41 copr_base 4.4 MiB python3-numpy x86_64 1:1.26.4-8.fc41 copr_base 43.8 MiB python3-pytest noarch 8.3.3-1.fc41 updates 20.8 MiB python3-requests noarch 2.32.3-3.fc41 copr_base 485.9 KiB python3-setuptools noarch 74.1.3-4.fc41 copr_base 8.4 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3.8 MiB harfbuzz x86_64 9.0.0-3.fc41 fedora 2.6 MiB hdf5 x86_64 1.12.1-20.fc41 fedora 8.4 MiB jbigkit-libs x86_64 2.1-30.fc41 fedora 117.6 KiB jsoncpp x86_64 1.9.5-8.fc41 fedora 253.4 KiB kernel-headers x86_64 6.11.3-300.fc41 fedora 6.4 MiB libX11 x86_64 1.8.10-2.fc41 fedora 1.3 MiB libX11-common noarch 1.8.10-2.fc41 fedora 1.1 MiB libXau x86_64 1.0.11-7.fc41 fedora 66.9 KiB libXpm x86_64 3.5.17-4.fc41 fedora 148.4 KiB libaec x86_64 1.1.3-1.fc41 fedora 98.1 KiB libaec-devel x86_64 1.1.3-1.fc41 fedora 12.5 KiB libaom x86_64 3.9.0-3.fc41 fedora 5.1 MiB libavif x86_64 1.0.4-7.fc41 fedora 183.8 KiB libb2 x86_64 0.98.1-12.fc41 fedora 42.2 KiB libdav1d x86_64 1.5.0-1.fc41 updates 1.7 MiB libgfortran x86_64 14.2.1-3.fc41 fedora 3.0 MiB libicu x86_64 74.2-2.fc41 fedora 34.9 MiB libicu-devel x86_64 74.2-2.fc41 fedora 5.6 MiB libimagequant x86_64 4.0.3-5.fc41 fedora 666.7 KiB libjpeg-turbo x86_64 3.0.2-3.fc41 fedora 776.9 KiB liblerc x86_64 4.0.0-7.fc41 fedora 607.5 KiB liblzf x86_64 3.6-29.fc41 fedora 53.8 KiB libmpc x86_64 1.3.1-6.fc41 fedora 164.7 KiB libpng x86_64 2:1.6.40-4.fc41 fedora 245.8 KiB libquadmath x86_64 14.2.1-3.fc41 fedora 325.9 KiB libquadmath-devel x86_64 14.2.1-3.fc41 fedora 21.9 KiB libstdc++-devel x86_64 14.2.1-3.fc41 fedora 15.4 MiB libtiff x86_64 4.6.0-6.fc41 fedora 606.0 KiB libuv x86_64 1:1.49.2-1.fc41 updates 565.0 KiB libvmaf x86_64 3.0.0-2.fc41 fedora 823.0 KiB libwebp x86_64 1.4.0-4.fc41 fedora 822.6 KiB libxcb x86_64 1.17.0-3.fc41 fedora 1.2 MiB libxcrypt-devel x86_64 4.4.36-10.fc41 updates 30.5 KiB mailcap noarch 2.1.54-7.fc41 fedora 86.0 KiB make x86_64 1:4.4.1-8.fc41 fedora 1.8 MiB mpdecimal x86_64 2.5.1-16.fc41 fedora 204.9 KiB ncurses x86_64 6.5-2.20240629.fc41 fedora 627.3 KiB nettle x86_64 3.10-3.fc41 fedora 793.0 KiB openblas x86_64 0.3.26-5.fc41 fedora 96.0 KiB openblas-openmp x86_64 0.3.26-5.fc41 fedora 39.4 MiB perl-AutoLoader noarch 5.74-512.fc41 updates 20.5 KiB perl-B x86_64 1.89-512.fc41 updates 498.0 KiB perl-B-Hooks-EndOfScope 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noarch 0.45-512.fc41 updates 82.3 KiB perl-I18N-Langinfo x86_64 0.24-512.fc41 updates 38.8 KiB perl-IO x86_64 1.55-512.fc41 updates 151.1 KiB perl-IO-Compress noarch 2.212-512.fc41 fedora 1.0 MiB perl-IO-HTML noarch 1.004-13.fc41 fedora 45.2 KiB perl-IO-Socket-IP noarch 0.42-512.fc41 fedora 98.7 KiB perl-IO-Socket-SSL noarch 2.089-1.fc41 fedora 703.3 KiB perl-IPC-Open3 noarch 1.22-512.fc41 updates 22.5 KiB perl-JSON noarch 4.10-6.fc41 fedora 270.5 KiB perl-JSON-XS x86_64 1:4.03-15.fc41 fedora 270.3 KiB perl-LWP-MediaTypes noarch 6.04-19.fc41 fedora 79.0 KiB perl-Locale-Maketext noarch 1.33-512.fc41 fedora 171.3 KiB perl-Locale-Maketext-Simple noarch 1:0.21-512.fc41 updates 12.8 KiB perl-MIME-Base32 noarch 1.303-21.fc41 fedora 30.7 KiB perl-MIME-Base64 x86_64 3.16-511.fc41 fedora 46.1 KiB perl-MRO-Compat noarch 0.15-10.fc41 fedora 43.0 KiB perl-Math-BigInt noarch 1:2.0030.03-3.fc41 fedora 957.7 KiB perl-Math-Complex noarch 1.62-512.fc41 updates 85.0 KiB perl-Module-CoreList noarch 1:5.20241020-1.fc41 updates 1.2 MiB perl-Module-Implementation noarch 0.09-40.fc41 fedora 24.7 KiB perl-Module-Load noarch 1:0.36-511.fc41 fedora 14.9 KiB perl-Module-Load-Conditional noarch 0.74-511.fc41 fedora 28.7 KiB perl-Module-Metadata noarch 1.000038-511.fc41 fedora 67.5 KiB perl-Module-Runtime noarch 0.016-23.fc41 fedora 30.4 KiB perl-Mozilla-CA noarch 20240730-1.fc41 fedora 9.8 KiB perl-Net-SSLeay x86_64 1.94-7.fc41 fedora 1.3 MiB perl-POSIX x86_64 2.20-512.fc41 updates 235.1 KiB perl-Package-Generator noarch 1.106-32.fc41 fedora 29.9 KiB perl-Package-Stash noarch 0.40-8.fc41 fedora 55.9 KiB perl-Package-Stash-XS x86_64 0.30-9.fc41 fedora 68.3 KiB perl-PadWalker x86_64 2.5-15.fc41 fedora 45.1 KiB perl-Params-Check noarch 1:0.38-511.fc41 fedora 27.6 KiB perl-Params-Classify x86_64 0.015-24.fc41 fedora 47.6 KiB perl-Params-Util x86_64 1.102-16.fc41 fedora 54.6 KiB perl-Params-ValidationCompiler noarch 0.31-6.fc41 fedora 91.1 KiB perl-PathTools x86_64 3.91-511.fc41 fedora 180.0 KiB perl-Pod-Escapes noarch 1:1.07-511.fc41 fedora 24.9 KiB perl-Pod-Html noarch 1.35-512.fc41 updates 42.2 KiB perl-Pod-Perldoc noarch 3.28.01-512.fc41 fedora 163.7 KiB perl-Pod-Simple noarch 1:3.45-511.fc41 fedora 560.9 KiB perl-Pod-Usage noarch 4:2.03-511.fc41 fedora 84.8 KiB perl-Ref-Util noarch 0.204-21.fc41 fedora 31.5 KiB perl-Ref-Util-XS x86_64 0.117-24.fc41 fedora 42.2 KiB perl-Role-Tiny noarch 2.002004-12.fc41 fedora 61.7 KiB perl-Scalar-List-Utils x86_64 5:1.68-1.fc41 updates 148.9 KiB perl-SelectSaver noarch 1.02-512.fc41 updates 2.2 KiB perl-Socket x86_64 4:2.038-511.fc41 fedora 124.0 KiB perl-Specio noarch 0.48-7.fc41 fedora 329.7 KiB perl-Storable x86_64 1:3.32-511.fc41 fedora 232.4 KiB perl-Sub-Exporter noarch 0.991-4.fc41 fedora 194.9 KiB perl-Sub-Exporter-Progressive noarch 0.001013-25.fc41 fedora 27.3 KiB perl-Sub-Identify x86_64 0.14-28.fc41 fedora 31.9 KiB perl-Sub-Install noarch 0.929-6.fc41 fedora 35.9 KiB perl-Symbol noarch 1.09-512.fc41 updates 6.8 KiB perl-Term-ANSIColor noarch 5.01-512.fc41 fedora 97.5 KiB perl-Term-Cap noarch 1.18-511.fc41 fedora 29.3 KiB perl-Text-ParseWords noarch 3.31-511.fc41 fedora 13.6 KiB perl-Text-Tabs+Wrap noarch 2024.001-511.fc41 fedora 22.6 KiB perl-Time-HiRes x86_64 4:1.9777-511.fc41 fedora 119.9 KiB perl-Time-Local noarch 2:1.350-511.fc41 fedora 69.0 KiB perl-TimeDate noarch 1:2.33-15.fc41 fedora 95.2 KiB perl-Try-Tiny noarch 0.32-1.fc41 fedora 67.3 KiB perl-Types-Serialiser noarch 1.01-12.fc41 fedora 22.9 KiB perl-URI noarch 5.30-1.fc41 fedora 256.9 KiB perl-Variable-Magic x86_64 0.64-3.fc41 fedora 130.6 KiB perl-XString x86_64 0.005-14.fc41 fedora 37.0 KiB perl-base noarch 2.27-512.fc41 updates 12.5 KiB perl-common-sense x86_64 3.7.5-18.fc41 fedora 47.0 KiB perl-constant noarch 1.33-512.fc41 fedora 26.2 KiB perl-if noarch 0.61.000-512.fc41 updates 5.8 KiB perl-interpreter x86_64 4:5.40.0-512.fc41 updates 122.3 KiB perl-lib x86_64 0.65-512.fc41 updates 8.5 KiB perl-libnet noarch 3.15-512.fc41 fedora 289.4 KiB perl-libs x86_64 4:5.40.0-512.fc41 updates 9.9 MiB perl-locale noarch 1.12-512.fc41 updates 6.5 KiB perl-mro x86_64 1.29-512.fc41 updates 45.6 KiB perl-namespace-autoclean noarch 0.29-19.fc41 fedora 41.1 KiB perl-namespace-clean noarch 0.27-27.fc41 fedora 38.7 KiB perl-overload noarch 1.37-512.fc41 updates 71.5 KiB perl-overloading noarch 0.02-512.fc41 updates 4.8 KiB perl-parent noarch 1:0.242-1.fc41 fedora 10.0 KiB perl-podlators noarch 1:6.0.2-2.fc41 fedora 317.5 KiB perl-vars noarch 1.05-512.fc41 updates 3.9 KiB perl-version x86_64 9:0.99.33-1.fc41 fedora 132.8 KiB perltidy noarch 20240903-1.fc41 fedora 3.9 MiB pyproject-rpm-macros noarch 1.16.1-1.fc41 copr_base 113.8 KiB python-pip-wheel noarch 24.3.1-1.fc41 copr_base 1.2 MiB python-rpm-macros noarch 3.13-3.fc41 fedora 22.1 KiB python3 x86_64 3.13.0-1.fc41 fedora 31.8 KiB python3-cached_property noarch 2.0.1-1.fc41 copr_base 34.8 KiB python3-charset-normalizer noarch 3.4.0-1.fc41 copr_base 322.1 KiB python3-idna noarch 3.9-2.fc41 copr_base 639.8 KiB python3-iniconfig noarch 1.1.1-24.fc41 copr_base 20.6 KiB python3-libs x86_64 3.13.0-1.fc41 fedora 40.3 MiB python3-packaging noarch 24.2-2.fc41 copr_base 558.2 KiB python3-pluggy noarch 1.5.0-1.fc41 copr_base 193.2 KiB python3-rpm-generators noarch 14-11.fc41 fedora 81.7 KiB python3-rpm-macros noarch 3.13-3.fc41 fedora 6.4 KiB python3-six noarch 1.16.0-24.fc41 copr_base 118.3 KiB python3-urllib3 noarch 2.2.3-5.fc41 copr_base 1.0 MiB rav1e-libs x86_64 0.7.1-4.fc41 fedora 3.0 MiB rhash x86_64 1.4.4-2.fc41 fedora 349.9 KiB svt-av1-libs x86_64 2.1.0-2.fc41 fedora 7.1 MiB tzdata noarch 2024a-9.fc41 fedora 1.7 MiB vim-filesystem noarch 2:9.1.825-1.fc41 updates 40.0 B xml-common noarch 0.6.3-65.fc41 fedora 78.4 KiB zlib-ng-compat-devel x86_64 2.1.7-3.fc41 fedora 106.8 KiB Transaction Summary: Installing: 279 packages Total size of inbound packages is 197 MiB. Need to download 197 MiB. After this operation, 789 MiB extra will be used (install 789 MiB, remove 0 B). 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[270/279] annobin-plugin-gcc-0:12.69-1. 100% | 9.9 MiB/s | 971.0 KiB | 00m00s [271/279] gcc-plugin-annobin-0:14.2.1-3 100% | 2.8 MiB/s | 55.1 KiB | 00m00s [272/279] annobin-docs-0:12.69-1.fc41.n 100% | 4.7 MiB/s | 91.8 KiB | 00m00s [273/279] pyproject-rpm-macros-0:1.16.1 100% | 5.5 MiB/s | 45.1 KiB | 00m00s [274/279] python-rpm-macros-0:3.13-3.fc 100% | 631.0 KiB/s | 17.7 KiB | 00m00s [275/279] python3-rpm-generators-0:14-1 100% | 1.6 MiB/s | 29.3 KiB | 00m00s [276/279] kernel-headers-0:6.11.3-300.f 100% | 5.8 MiB/s | 1.6 MiB | 00m00s [277/279] python3-rpm-macros-0:3.13-3.f 100% | 691.3 KiB/s | 12.4 KiB | 00m00s [278/279] cmake-rpm-macros-0:3.30.5-1.f 100% | 247.0 KiB/s | 16.8 KiB | 00m00s [279/279] glib2-0:2.82.2-1.fc41.x86_64 100% | 1.9 MiB/s | 3.0 MiB | 00m02s -------------------------------------------------------------------------------- [279/279] Total 100% | 21.4 MiB/s | 196.8 MiB | 00m09s Running transaction [ 1/281] Verify package files 100% | 412.0 B/s | 279.0 B | 00m01s [ 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checks for 16 packages from repository: copr_base Complete! Finish: build setup for morphio-3.4.0-1.fc41.src.rpm Start: rpmbuild morphio-3.4.0-1.fc41.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1731369600 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.RdrLU7 + umask 022 + cd /builddir/build/BUILD/morphio-3.4.0-build + test -d /builddir/build/BUILD/morphio-3.4.0-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/morphio-3.4.0-build + /usr/bin/rm -rf /builddir/build/BUILD/morphio-3.4.0-build + /usr/bin/mkdir -p /builddir/build/BUILD/morphio-3.4.0-build + /usr/bin/mkdir -p /builddir/build/BUILD/morphio-3.4.0-build/SPECPARTS + RPM_EC=0 ++ jobs -p + exit 0 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.a8j0vk + umask 022 + cd /builddir/build/BUILD/morphio-3.4.0-build + cd /builddir/build/BUILD/morphio-3.4.0-build + rm -rf MorphIO-3.4.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/MorphIO-3.4.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd MorphIO-3.4.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/stop-them-using-a-random-env-var.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/remove-upstreams-flags.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/install-python-shared-object.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/stop-setup.py-from-cmake-build.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/pytest-float32.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/use-lib_install_dir.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/allow_use_of_external_ghc_filesystem.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/dont_use_cmake_for_finding_ghc_filesystem.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + rm -rvf 3rdparty/GSL_LITE removed directory '3rdparty/GSL_LITE' + sed -r -i /GSL_LITE/d MANIFEST.in + sed -r -i '/director.*\(.*(gsl-lite|GSL_LITE).*\)/d' 3rdparty/CMakeLists.txt + sed -r -i -e /TARGET_PROPERTY:gsl-lite,INTERFACE_INCLUDE_DIRECTORIES/d -e 's/PUBLIC[[:blank:]]+gsl-lite[[:blank:]]+(PRIVATE)/\1/' src/CMakeLists.txt + grep -ErIl '#[[:blank:]]*include[[:blank:]]+["<]gsl/gsl[">]' . + xargs -r sed -r -i 's@(#[[:blank:]]*include[[:blank:]]+["<]gsl/gsl)([">])@\1-lite\.hpp\2@' + rm -rvf 3rdparty/lexertl + ln -s /usr/include/lexertl 3rdparty/ + find . -type f -name .gitignore -print -delete ./.gitignore ./doc/source/doxygen/.gitignore + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.5YQl3W + umask 022 + cd /builddir/build/BUILD/morphio-3.4.0-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 MorphIO-3.4.0 + export SETUPTOOLS_SCM_PRETEND_VERSION=3.4.0 + SETUPTOOLS_SCM_PRETEND_VERSION=3.4.0 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 + /usr/bin/cmake -S . -B redhat-linux-build -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -DEXTERNAL_PYBIND11:BOOL=TRUE -DEXTERNAL_HIGHFIVE:BOOL=TRUE -DEXTERNAL_GHC_FILESYSTEM:BOOL=TRUE -DMORPHIO_USE_DOUBLE:BOOL=TRUE -DBUILD_BINDINGS:BOOL=TRUE -DMorphIO_CXX_WARNINGS:BOOL=FALSE -DMORPHIO_TESTS:BOOL=TRUE -DEXTERNAL_CATCH2:BOOL=TRUE -DMORPHIO_ENABLE_COVERAGE:BOOL=TRUE -DMORPHIO_USE_DOUBLE:BOOL=TRUE -DMORPHIO_VERSION_STRING:STRING=3.4.0 -GNinja -Wno-dev -- The C compiler identification is GNU 14.2.1 -- The CXX compiler identification is GNU 14.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Floating Point Type: double -- HIGHFIVE 2.10.0: (Re)Detecting Highfive dependencies (HIGHFIVE_USE_INSTALL_DEPS=NO) -- Found HDF5: /usr/lib64/libhdf5.so (found version "1.12.1") -- Found Boost: /usr/include (found version "1.83.0") found components: system serialization -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.13", minimum required is "3.7") -- Found PythonLibs: /usr/lib64/libpython3.13.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.13.6") -- Performing Test HAVE_fprofile_abs_path -- Performing Test HAVE_fprofile_abs_path - Success CMake Warning at CMake/CodeCoverage.cmake:206 (message): Code coverage results with an optimised (non-Debug) build may be misleading Call Stack (most recent call first): src/CMakeLists.txt:85 (include) -- Warning: this does not have an effect - use NO_SYSTEM_FROM_IMPORTED if using imported targets -- Found Python3: /usr/bin/python3.13 (found version "3.13.0") found components: Interpreter CMake Warning at CMake/CodeCoverage.cmake:206 (message): Code coverage results with an optimised (non-Debug) build may be misleading Call Stack (most recent call first): tests/CMakeLists.txt:43 (include) -- Configuring done (1.7s) -- Generating done (0.0s) -- Build files have been written to: /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/redhat-linux-build CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_RELEASE CMAKE_C_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP INCLUDE_INSTALL_DIR LIB_SUFFIX SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR + /usr/bin/cmake --build redhat-linux-build -j2 --verbose Change Dir: '/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/redhat-linux-build' Run Build Command(s): /usr/bin/ninja-build -v -j 2 [1/64] /usr/bin/g++ -DMORPHIO_USE_DOUBLE -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0 -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/../include -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/3rdparty/lexertl14/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++14 -fPIC -g --coverage -fprofile-abs-path -MD -MT src/CMakeFiles/morphio_obj.dir/dendritic_spine.cpp.o -MF src/CMakeFiles/morphio_obj.dir/dendritic_spine.cpp.o.d -o src/CMakeFiles/morphio_obj.dir/dendritic_spine.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/dendritic_spine.cpp [2/64] /usr/bin/g++ -DMORPHIO_USE_DOUBLE -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0 -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/../include -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/3rdparty/lexertl14/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++14 -fPIC -g --coverage -fprofile-abs-path -MD -MT src/CMakeFiles/morphio_obj.dir/endoplasmic_reticulum.cpp.o -MF src/CMakeFiles/morphio_obj.dir/endoplasmic_reticulum.cpp.o.d -o src/CMakeFiles/morphio_obj.dir/endoplasmic_reticulum.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/endoplasmic_reticulum.cpp [3/64] /usr/bin/g++ -DMORPHIO_USE_DOUBLE -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0 -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/../include -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/3rdparty/lexertl14/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++14 -fPIC -g --coverage -fprofile-abs-path -MD -MT src/CMakeFiles/morphio_obj.dir/enums.cpp.o -MF src/CMakeFiles/morphio_obj.dir/enums.cpp.o.d -o src/CMakeFiles/morphio_obj.dir/enums.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/enums.cpp [4/64] /usr/bin/g++ -DMORPHIO_USE_DOUBLE -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0 -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/../include -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/3rdparty/lexertl14/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++14 -fPIC -g --coverage -fprofile-abs-path -MD -MT src/CMakeFiles/morphio_obj.dir/errorMessages.cpp.o -MF src/CMakeFiles/morphio_obj.dir/errorMessages.cpp.o.d -o src/CMakeFiles/morphio_obj.dir/errorMessages.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/errorMessages.cpp [5/64] /usr/bin/g++ -DMORPHIO_USE_DOUBLE -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0 -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/../include -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/3rdparty/lexertl14/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++14 -fPIC -g --coverage -fprofile-abs-path -MD -MT src/CMakeFiles/morphio_obj.dir/collection.cpp.o -MF src/CMakeFiles/morphio_obj.dir/collection.cpp.o.d -o src/CMakeFiles/morphio_obj.dir/collection.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/collection.cpp [6/64] /usr/bin/g++ -DMORPHIO_USE_DOUBLE -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0 -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/../include -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/3rdparty/lexertl14/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++14 -fPIC -g --coverage -fprofile-abs-path -MD -MT src/CMakeFiles/morphio_obj.dir/error_message_generation.cpp.o -MF src/CMakeFiles/morphio_obj.dir/error_message_generation.cpp.o.d -o src/CMakeFiles/morphio_obj.dir/error_message_generation.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/error_message_generation.cpp [7/64] /usr/bin/g++ -DMORPHIO_USE_DOUBLE -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0 -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/../include -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/3rdparty/lexertl14/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++14 -fPIC -g --coverage -fprofile-abs-path -MD -MT src/CMakeFiles/morphio_obj.dir/glial_cell.cpp.o -MF src/CMakeFiles/morphio_obj.dir/glial_cell.cpp.o.d -o src/CMakeFiles/morphio_obj.dir/glial_cell.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/glial_cell.cpp [8/64] /usr/bin/g++ -DMORPHIO_USE_DOUBLE -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0 -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/../include -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/3rdparty/lexertl14/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++14 -fPIC -g --coverage -fprofile-abs-path -MD -MT src/CMakeFiles/morphio_obj.dir/mito_section.cpp.o -MF src/CMakeFiles/morphio_obj.dir/mito_section.cpp.o.d -o src/CMakeFiles/morphio_obj.dir/mito_section.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/mito_section.cpp [9/64] /usr/bin/g++ -DMORPHIO_USE_DOUBLE -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0 -I/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/src/../include -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/3rdparty/lexertl14/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++14 -fPIC -g --coverage -fprofile-abs-path -MD -MT src/CMakeFiles/morphio_obj.dir/mitochondria.cpp.o -MF 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-fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++17 -MD -MT tests/CMakeFiles/unittests.dir/test_mutable_morphology.cpp.o -MF tests/CMakeFiles/unittests.dir/test_mutable_morphology.cpp.o.d -o tests/CMakeFiles/unittests.dir/test_mutable_morphology.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/tests/test_mutable_morphology.cpp [57/64] /usr/bin/g++ -DBOOST_ALL_NO_LIB -DH5_USE_BOOST -DHIGHFIVE_HAS_CONCEPTS=0 -DMORPHIO_USE_DOUBLE -DMPI_NO_CPPBIND -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++17 -MD -MT tests/CMakeFiles/unittests.dir/test_properties.cpp.o -MF tests/CMakeFiles/unittests.dir/test_properties.cpp.o.d -o tests/CMakeFiles/unittests.dir/test_properties.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/tests/test_properties.cpp [58/64] /usr/bin/g++ -DBOOST_ALL_NO_LIB -DH5_USE_BOOST -DHIGHFIVE_HAS_CONCEPTS=0 -DMORPHIO_USE_DOUBLE -DMPI_NO_CPPBIND -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++17 -MD -MT tests/CMakeFiles/unittests.dir/test_soma.cpp.o -MF tests/CMakeFiles/unittests.dir/test_soma.cpp.o.d -o tests/CMakeFiles/unittests.dir/test_soma.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/tests/test_soma.cpp [59/64] /usr/bin/g++ -DBOOST_ALL_NO_LIB -DH5_USE_BOOST -DHIGHFIVE_HAS_CONCEPTS=0 -DMORPHIO_USE_DOUBLE -DMPI_NO_CPPBIND -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++17 -MD -MT tests/CMakeFiles/unittests.dir/test_swc_reader.cpp.o -MF tests/CMakeFiles/unittests.dir/test_swc_reader.cpp.o.d -o tests/CMakeFiles/unittests.dir/test_swc_reader.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/tests/test_swc_reader.cpp [60/64] /usr/bin/g++ -DBOOST_ALL_NO_LIB -DH5_USE_BOOST -DHIGHFIVE_HAS_CONCEPTS=0 -DMORPHIO_USE_DOUBLE -DMPI_NO_CPPBIND -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++17 -MD -MT tests/CMakeFiles/unittests.dir/test_utilities.cpp.o -MF tests/CMakeFiles/unittests.dir/test_utilities.cpp.o.d -o tests/CMakeFiles/unittests.dir/test_utilities.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/tests/test_utilities.cpp [61/64] /usr/bin/cmake -E cmake_symlink_library src/libmorphio.so.0.0.0 src/libmorphio.so.0.0.0 src/libmorphio.so && : [62/64] /usr/bin/g++ -DBOOST_ALL_NO_LIB -DH5_USE_BOOST -DHIGHFIVE_HAS_CONCEPTS=0 -DMORPHIO_USE_DOUBLE -DMPI_NO_CPPBIND -isystem /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -std=c++17 -MD -MT tests/CMakeFiles/unittests.dir/test_vasculature_morphology.cpp.o -MF tests/CMakeFiles/unittests.dir/test_vasculature_morphology.cpp.o.d -o tests/CMakeFiles/unittests.dir/test_vasculature_morphology.cpp.o -c /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/tests/test_vasculature_morphology.cpp [63/64] : && /usr/bin/g++ -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -flto -shared -o binds/python/_morphio.cpython-313-x86_64-linux-gnu.so binds/python/CMakeFiles/_morphio.dir/morphio.cpp.o binds/python/CMakeFiles/_morphio.dir/bind_enums.cpp.o binds/python/CMakeFiles/_morphio.dir/bind_immutable.cpp.o binds/python/CMakeFiles/_morphio.dir/bind_misc.cpp.o binds/python/CMakeFiles/_morphio.dir/bind_mutable.cpp.o binds/python/CMakeFiles/_morphio.dir/bind_vasculature.cpp.o binds/python/CMakeFiles/_morphio.dir/bind_warnings_exceptions.cpp.o binds/python/CMakeFiles/_morphio.dir/bindings_utils.cpp.o src/libmorphio_static.a -lgcov -lhdf5 && cd /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/redhat-linux-build/binds/python && /usr/bin/strip /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/redhat-linux-build/binds/python/_morphio.cpython-313-x86_64-linux-gnu.so [64/64] : && /usr/bin/g++ -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -rdynamic tests/CMakeFiles/unittests.dir/main.cpp.o tests/CMakeFiles/unittests.dir/test_collection.cpp.o tests/CMakeFiles/unittests.dir/test_enums.cpp.o tests/CMakeFiles/unittests.dir/test_immutable_morphology.cpp.o tests/CMakeFiles/unittests.dir/test_mitochondria.cpp.o tests/CMakeFiles/unittests.dir/test_morphology_readers.cpp.o tests/CMakeFiles/unittests.dir/test_mutable_morphology.cpp.o tests/CMakeFiles/unittests.dir/test_point_utils.cpp.o tests/CMakeFiles/unittests.dir/test_properties.cpp.o tests/CMakeFiles/unittests.dir/test_soma.cpp.o tests/CMakeFiles/unittests.dir/test_swc_reader.cpp.o tests/CMakeFiles/unittests.dir/test_utilities.cpp.o tests/CMakeFiles/unittests.dir/test_vasculature_morphology.cpp.o -o /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/bin/unittests src/libmorphio_static.a -lstdc++fs -lhdf5 -lgcov && : + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -sP' /usr/lib/python3.13/site-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section' Traceback (most recent call last): File "/usr/lib/python3.13/site-packages/setuptools_scm/_integration/pyproject_reading.py", line 36, in read_pyproject section = defn.get("tool", {})[tool_name] ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ KeyError: 'setuptools_scm' running build running build_py creating build creating build/lib creating build/lib/morphio copying morphio/__init__.py -> build/lib/morphio creating build/lib/morphio/mut copying morphio/mut/__init__.py -> build/lib/morphio/mut creating build/lib/morphio/vasculature copying morphio/vasculature/__init__.py -> build/lib/morphio/vasculature + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.qGalAs + umask 022 + cd /builddir/build/BUILD/morphio-3.4.0-build + '[' /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT ++ dirname /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT + mkdir -p /builddir/build/BUILD/morphio-3.4.0-build + mkdir /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 MorphIO-3.4.0 + export SETUPTOOLS_SCM_PRETEND_VERSION=3.4.0 + SETUPTOOLS_SCM_PRETEND_VERSION=3.4.0 + DESTDIR=/builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT + /usr/bin/cmake --install redhat-linux-build -- Install configuration: "" -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/collection.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/dendritic_spine.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/endoplasmic_reticulum.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/enums.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/errorMessages.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/exceptions.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/glial_cell.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/mito_section.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/mitochondria.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/morphology.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/mut -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/mut/dendritic_spine.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/mut/endoplasmic_reticulum.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/mut/glial_cell.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/mut/mito_section.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/mut/mitochondria.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/mut/modifiers.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/mut/morphology.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/mut/section.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/mut/soma.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/mut/writers.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/properties.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/section.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/section_base.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/section_iterators.hpp -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/soma.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/types.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/vasc -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/vasc/iterators.hpp -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/vasc/properties.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/vasc/section.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/vasc/vasculature.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/vector_types.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/version.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/include/morphio/warning_handling.h -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/cmake/MorphIO/MorphIOTargets.cmake -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/cmake/MorphIO/MorphIOTargets-noconfig.cmake -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/cmake/MorphIO/MorphIOConfig.cmake -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/libmorphio.so.0.0.0 -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/libmorphio.so -- Installing: /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/morphio/_morphio.cpython-313-x86_64-linux-gnu.so + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + /usr/bin/python3 setup.py install -O1 --skip-build --root /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT --prefix /usr /usr/lib/python3.13/site-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING setuptools_scm.pyproject_reading toml section missing 'pyproject.toml does not contain a tool.setuptools_scm section' Traceback (most recent call last): File "/usr/lib/python3.13/site-packages/setuptools_scm/_integration/pyproject_reading.py", line 36, in read_pyproject section = defn.get("tool", {})[tool_name] ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ KeyError: 'setuptools_scm' running install /usr/lib/python3.13/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. Follow the current Python packaging guidelines when building Python RPM packages. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html and https://docs.fedoraproject.org/en-US/packaging-guidelines/Python/ for details. ******************************************************************************** !! self.initialize_options() running install_lib creating /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib creating /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13 creating /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages creating /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio copying build/lib/morphio/__init__.py -> /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio creating /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/mut copying build/lib/morphio/mut/__init__.py -> /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/mut creating /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/vasculature copying build/lib/morphio/vasculature/__init__.py -> /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/vasculature byte-compiling /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/__init__.py to __init__.cpython-313.pyc byte-compiling /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/mut/__init__.py to __init__.cpython-313.pyc byte-compiling /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/vasculature/__init__.py to __init__.cpython-313.pyc writing byte-compilation script '/tmp/tmpn1yzjb3d.py' /usr/bin/python3 /tmp/tmpn1yzjb3d.py removing /tmp/tmpn1yzjb3d.py running install_egg_info running egg_info creating morphio.egg-info writing morphio.egg-info/PKG-INFO writing dependency_links to morphio.egg-info/dependency_links.txt writing requirements to morphio.egg-info/requires.txt writing top-level names to morphio.egg-info/top_level.txt writing manifest file 'morphio.egg-info/SOURCES.txt' reading manifest file 'morphio.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '3rdparty/HighFive/CMakeLists.txt' warning: no files found matching '*' under directory '3rdparty/HighFive/include' warning: no files found matching '*' under directory '3rdparty/HighFive/CMake' warning: no files found matching '*' under directory '3rdparty/HighFive/doc' warning: no files found matching '3rdparty/lexertl14/CMakeLists.txt' warning: no files found matching '*' under directory '3rdparty/lexertl14/include/lexertl' warning: no files found matching '*' under directory 'binds/python/pybind11/include' warning: no files found matching '*.cmake' under directory 'binds/python/pybind11/tools' warning: no files found matching 'binds/python/pybind11/CMakeLists.txt' warning: no files found matching 'binds/python/pybind11/LICENSE' no previously-included directories found matching 'ci' no previously-included directories found matching 'doc' no previously-included directories found matching 'scripts' adding license file 'LICENSE.txt' adding license file 'AUTHORS.txt' no previously-included directories found matching 'examples' writing manifest file 'morphio.egg-info/SOURCES.txt' Copying morphio.egg-info to /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio-3.4.0-py3.13.egg-info running install_scripts + rm -rfv /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/bin/__pycache__ + '[' /usr/lib/python3.13/site-packages '!=' /usr/lib64/python3.13/site-packages ']' + mv -v /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/__init__.py /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/__pycache__ /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/mut /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/vasculature /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/morphio renamed '/builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/__init__.py' -> '/builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/morphio/__init__.py' renamed '/builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/__pycache__' -> '/builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/morphio/__pycache__' renamed '/builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/mut' -> '/builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/morphio/mut' renamed '/builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio/vasculature' -> '/builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/morphio/vasculature' + mv -v /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio-3.4.0-py3.13.egg-info /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/ renamed '/builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13/site-packages/morphio-3.4.0-py3.13.egg-info' -> '/builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/morphio-3.4.0-py3.13.egg-info' + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 3.4.0-1.fc41 --unique-debug-suffix -3.4.0-1.fc41.x86_64 --unique-debug-src-base morphio-3.4.0-1.fc41.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0 find-debuginfo: starting Extracting debug info from 1 files DWARF-compressing 1 files sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/morphio-3.4.0-1.fc41.x86_64 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/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/python3.13 using python3.13 Bytecompiling .py files below /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib/python3.13 using python3.13 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-determinism --brp -j2 /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/morphio/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/morphio/mut/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents /builddir/build/BUILD/morphio-3.4.0-build/BUILDROOT/usr/lib64/python3.13/site-packages/morphio/vasculature/__pycache__/__init__.cpython-313.pyc: rewriting with normalized contents Scanned 37 directories and 136 files, processed 3 inodes, 3 modified (0 replaced + 3 rewritten), 0 unsupported format, 0 errors Reading /builddir/build/BUILD/morphio-3.4.0-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.WZzsGR + umask 022 + cd /builddir/build/BUILD/morphio-3.4.0-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -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 MorphIO-3.4.0 + export SETUPTOOLS_SCM_PRETEND_VERSION=3.4.0 + SETUPTOOLS_SCM_PRETEND_VERSION=3.4.0 + /usr/bin/ctest --test-dir redhat-linux-build --output-on-failure --force-new-ctest-process -j2 -VV Internal ctest changing into directory: /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/redhat-linux-build UpdateCTestConfiguration from :/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/redhat-linux-build/DartConfiguration.tcl UpdateCTestConfiguration from :/builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/redhat-linux-build/DartConfiguration.tcl Test project /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/redhat-linux-build Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: unittests 1: Test command: /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/bin/unittests 1: Working Directory: /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/tests 1: Test timeout computed to be: 10000000 1: 1: $STRING$:2:warning 1: Warning: found a disconnected neurite. 1: Neurites are not supposed to have parentId: -1 1: (although this is normal if this neuron has no soma) 1: 1: $STRING$:2:warning 1: Warning: found a disconnected neurite. 1: Neurites are not supposed to have parentId: -1 1: (although this is normal if this neuron has no soma) 1: 1: $STRING$:2:warning 1: Warning: found a disconnected neurite. 1: Neurites are not supposed to have parentId: -1 1: (although this is normal if this neuron has no soma) 1: 1: $STRING$:2:warning 1: Warning: found a disconnected neurite. 1: Neurites are not supposed to have parentId: -1 1: (although this is normal if this neuron has no soma) 1: 1: $STRING$:4:warning 1: Warning: found a disconnected neurite. 1: Neurites are not supposed to have parentId: -1 1: (although this is normal if this neuron has no soma) 1: 1: $STRING$:0:warning 1: Warning: no soma found in file 1: 1: $STRING$:3:warning 1: Warning: Type changed within section, without bifurcation 1: 1: $STRING$:4:warning 1: Warning: Type changed within section, without bifurcation 1: 1: $STRING$:5:warning 1: Warning: Type changed within section, without bifurcation 1: 1: data/single_point_root.asc:0:warning 1: Warning: no soma found in file 1: 1: Warning: section 1 is the only child of section: 0 1: It will be merged with the parent section 1: 1: Warning: section 2 is the only child of section: 0 1: It will be merged with the parent section 1: 1: Warning: section 3 is the only child of section: 0 1: It will be merged with the parent section 1: 1: Warning: Skipping an attempt to write an empty morphology. 1: 1: Warning: writing file without a soma 1: 1: Warning: writing soma set to SOMA_UNDEFINED 1: 1: Soma must be stacked cylinders or a point: see https://github.com/BlueBrain/MorphIO/issues/457 1: 1: Three Point Soma: Only one column has the same coordinates. 1: 1: data/h5/v1/Neuron-no-soma.h5:0:warning 1: Warning: no soma found in file 1: 1: data/h5/v1/simple-dendritric-spine.h5:0:warning 1: Warning: no soma found in file 1: 1: data/h5/v1/single-neurite.h5:0:warning 1: Warning: no soma found in file 1: 1: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1: unittests is a Catch v2.13.10 host application. 1: Run with -? for options 1: 1: ------------------------------------------------------------------------------- 1: LoadSWCMorphologyLocale 1: ------------------------------------------------------------------------------- 1: /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/tests/test_morphology_readers.cpp:213 1: ............................................................................... 1: 1: /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/tests/test_morphology_readers.cpp:213: FAILED: 1: due to unexpected exception with message: 1: locale::facet::_S_create_c_locale name not valid 1: 1: 1: data/markers.asc:0:warning 1: Warning: no soma found in file 1: 1: data/annotations.asc:0:warning 1: Warning: no soma found in file 1: 1: Warning: section 1 is the only child of section: 0 1: It will be merged with the parent section 1: 1: data/h5/v1/simple-dendritric-spine.h5:0:warning 1: Warning: no soma found in file 1: 1: data/h5/v1/simple-dendritric-spine.h5:0:warning 1: Warning: no soma found in file 1: 1: data/h5/v1/simple-dendritric-spine.h5:0:warning 1: Warning: no soma found in file 1: 1: HDF5 GROUP:0:warning 1: Warning: no soma found in file 1: 1: data/h5/v1/simple-dendritric-spine.h5:0:warning 1: Warning: no soma found in file 1: 1: Warning: while appending section: 2 to parent: 1 1: The section first point should be parent section last point: 1: : X Y Z Diameter 1: parent last point :[0.000000, 15.900000, 0.000000, 2.400000] 1: child first point :[0.000000, 13.200000, 0.000000, 2.300000] 1: 1: 1: data/h5/v1/simple-dendritric-spine.h5:0:warning 1: Warning: no soma found in file 1: 1: Warning: while appending section: 2 to parent: 1 1: The section first point should be parent section last point: 1: : X Y Z Diameter 1: parent last point :[0.000000, 15.900000, 0.000000, 2.400000] 1: child first point :[0.000000, 13.200000, 0.000000, 2.300000] 1: 1: 1: data/h5/v1/simple-dendritric-spine.h5:0:warning 1: Warning: no soma found in file 1: 1: Warning: while appending section: 2 to parent: 1 1: The section first point should be parent section last point: 1: : X Y Z Diameter 1: parent last point :[0.000000, 15.900000, 0.000000, 2.400000] 1: child first point :[0.000000, 13.200000, 0.000000, 2.300000] 1: 1: 1: HDF5 GROUP:0:warning 1: Warning: no soma found in file 1: 1: Warning: while appending section: 2 to parent: 1 1: The section first point should be parent section last point: 1: : X Y Z Diameter 1: parent last point :[0.000000, 15.900000, 0.000000, 2.400000] 1: child first point :[0.000000, 13.200000, 0.000000, 2.300000] 1: 1: 1: data/h5/v1/simple-dendritric-spine.h5:0:warning 1: Warning: no soma found in file 1: 1: data/h5/v1/simple-dendritric-spine.h5:0:warning 1: Warning: no soma found in file 1: 1: HDF5 GROUP:0:warning 1: Warning: no soma found in file 1: 1: HDF5 GROUP:0:warning 1: Warning: no soma found in file 1: =============================================================================== 1: test cases: 60 | 59 passed | 1 failed 1: assertions: 470 | 469 passed | 1 failed 1: 1/1 Test #1: unittests ........................***Failed 0.08 sec $STRING$:2:warning Warning: found a disconnected neurite. Neurites are not supposed to have parentId: -1 (although this is normal if this neuron has no soma) $STRING$:2:warning Warning: found a disconnected neurite. Neurites are not supposed to have parentId: -1 (although this is normal if this neuron has no soma) $STRING$:2:warning Warning: found a disconnected neurite. Neurites are not supposed to have parentId: -1 (although this is normal if this neuron has no soma) $STRING$:2:warning Warning: found a disconnected neurite. Neurites are not supposed to have parentId: -1 (although this is normal if this neuron has no soma) $STRING$:4:warning Warning: found a disconnected neurite. Neurites are not supposed to have parentId: -1 (although this is normal if this neuron has no soma) $STRING$:0:warning Warning: no soma found in file $STRING$:3:warning Warning: Type changed within section, without bifurcation $STRING$:4:warning Warning: Type changed within section, without bifurcation $STRING$:5:warning Warning: Type changed within section, without bifurcation data/single_point_root.asc:0:warning Warning: no soma found in file Warning: section 1 is the only child of section: 0 It will be merged with the parent section Warning: section 2 is the only child of section: 0 It will be merged with the parent section Warning: section 3 is the only child of section: 0 It will be merged with the parent section Warning: Skipping an attempt to write an empty morphology. Warning: writing file without a soma Warning: writing soma set to SOMA_UNDEFINED Soma must be stacked cylinders or a point: see https://github.com/BlueBrain/MorphIO/issues/457 Three Point Soma: Only one column has the same coordinates. data/h5/v1/Neuron-no-soma.h5:0:warning Warning: no soma found in file data/h5/v1/simple-dendritric-spine.h5:0:warning Warning: no soma found in file data/h5/v1/single-neurite.h5:0:warning Warning: no soma found in file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ unittests is a Catch v2.13.10 host application. Run with -? for options ------------------------------------------------------------------------------- LoadSWCMorphologyLocale ------------------------------------------------------------------------------- /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/tests/test_morphology_readers.cpp:213 ............................................................................... /builddir/build/BUILD/morphio-3.4.0-build/MorphIO-3.4.0/tests/test_morphology_readers.cpp:213: FAILED: due to unexpected exception with message: locale::facet::_S_create_c_locale name not valid data/markers.asc:0:warning Warning: no soma found in file data/annotations.asc:0:warning Warning: no soma found in file Warning: section 1 is the only child of section: 0 It will be merged with the parent section data/h5/v1/simple-dendritric-spine.h5:0:warning Warning: no soma found in file data/h5/v1/simple-dendritric-spine.h5:0:warning Warning: no soma found in file data/h5/v1/simple-dendritric-spine.h5:0:warning Warning: no soma found in file HDF5 GROUP:0:warning Warning: no soma found in file data/h5/v1/simple-dendritric-spine.h5:0:warning Warning: no soma found in file Warning: while appending section: 2 to parent: 1 The section first point should be parent section last point: : X Y Z Diameter parent last point :[0.000000, 15.900000, 0.000000, 2.400000] child first point :[0.000000, 13.200000, 0.000000, 2.300000] data/h5/v1/simple-dendritric-spine.h5:0:warning Warning: no soma found in file Warning: while appending section: 2 to parent: 1 The section first point should be parent section last point: : X Y Z Diameter parent last point :[0.000000, 15.900000, 0.000000, 2.400000] child first point :[0.000000, 13.200000, 0.000000, 2.300000] data/h5/v1/simple-dendritric-spine.h5:0:warning Warning: no soma found in file Warning: while appending section: 2 to parent: 1 The section first point should be parent section last point: : X Y Z Diameter parent last point :[0.000000, 15.900000, 0.000000, 2.400000] child first point :[0.000000, 13.200000, 0.000000, 2.300000] HDF5 GROUP:0:warning Warning: no soma found in file Warning: while appending section: 2 to parent: 1 The section first point should be parent section last point: : X Y Z Diameter parent last point :[0.000000, 15.900000, 0.000000, 2.400000] child first point :[0.000000, 13.200000, 0.000000, 2.300000] data/h5/v1/simple-dendritric-spine.h5:0:warning Warning: no soma found in file data/h5/v1/simple-dendritric-spine.h5:0:warning Warning: no soma found in file HDF5 GROUP:0:warning Warning: no soma found in file HDF5 GROUP:0:warning Warning: no soma found in file =============================================================================== test cases: 60 | 59 passed | 1 failed assertions: 470 | 469 passed | 1 failed 0% tests passed, 1 tests failed out of 1 Total Test time (real) = 0.08 sec The following tests FAILED: 1 - unittests (Failed) Errors while running CTest error: Bad exit status from /var/tmp/rpm-tmp.WZzsGR (%check) Bad exit status from /var/tmp/rpm-tmp.WZzsGR (%check) RPM build errors: Finish: rpmbuild morphio-3.4.0-1.fc41.src.rpm Finish: build phase for morphio-3.4.0-1.fc41.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-41-x86_64-1731409031.927648/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names ERROR: Exception(/var/lib/copr-rpmbuild/results/morphio-3.4.0-1.fc41.src.rpm) Config(fedora-41-x86_64) 3 minutes 43 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_failure=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot ERROR: Command failed: # /usr/bin/systemd-nspawn -q -M 5391c83d443b4333bd64b767ae17552a -D /var/lib/mock/fedora-41-x86_64-1731409031.927648/root -a -u mockbuild --capability=cap_ipc_lock --rlimit=RLIMIT_NOFILE=10240 --capability=cap_ipc_lock --bind=/tmp/mock-resolv.md3j7gma:/etc/resolv.conf --bind=/dev/btrfs-control --bind=/dev/mapper/control --bind=/dev/fuse --bind=/dev/loop-control --bind=/dev/loop0 --bind=/dev/loop1 --bind=/dev/loop2 --bind=/dev/loop3 --bind=/dev/loop4 --bind=/dev/loop5 --bind=/dev/loop6 --bind=/dev/loop7 --bind=/dev/loop8 --bind=/dev/loop9 --bind=/dev/loop10 --bind=/dev/loop11 --console=pipe --setenv=TERM=vt100 --setenv=SHELL=/bin/bash --setenv=HOME=/builddir --setenv=HOSTNAME=mock --setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin '--setenv=PROMPT_COMMAND=printf "\033]0;\007"' '--setenv=PS1= \s-\v\$ ' --setenv=LANG=C.UTF-8 --resolv-conf=off bash --login -c '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/originals/morphio.spec' Copr build error: Build failed