Warning: Permanently added '3.237.8.157' (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/9654123-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64 Version: 1.6 PID: 51268 Logging PID: 51270 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 9654123, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'b4cb2d476ea37477f362f60fa50b5a90408c551f', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/churchyard/setuptools-80.9.0:custom:isolated/hmmer', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'hmmer', 'package_version': '3.3.2-11', 'project_dirname': 'setuptools-80.9.0:custom:isolated', 'project_name': 'setuptools-80.9.0', 'project_owner': 'churchyard', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/churchyard/setuptools-80.9.0/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}, {'baseurl': 'https://download.copr.fedorainfracloud.org/results/churchyard/setuptools-80.9.0:custom:isolated/fedora-rawhide-x86_64/', 'id': 'copr_coprdir', 'name': 'Coprdir repository', 'priority': None}, {'baseurl': 'http://kojipkgs.fedoraproject.org/repos/f44-build/latest/$basearch/', 'id': 'http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch', 'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch'}], 'sandbox': 'churchyard/setuptools-80.9.0--churchyard', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'churchyard', 'tags': [], 'task_id': '9654123-fedora-rawhide-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/churchyard/setuptools-80.9.0:custom:isolated/hmmer /var/lib/copr-rpmbuild/workspace/workdir-raqbnmhq/hmmer --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/churchyard/setuptools-80.9.0:custom:isolated/hmmer', '/var/lib/copr-rpmbuild/workspace/workdir-raqbnmhq/hmmer', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-raqbnmhq/hmmer'... Running: git checkout b4cb2d476ea37477f362f60fa50b5a90408c551f -- cmd: ['git', 'checkout', 'b4cb2d476ea37477f362f60fa50b5a90408c551f', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-raqbnmhq/hmmer rc: 0 stdout: stderr: Note: switching to 'b4cb2d476ea37477f362f60fa50b5a90408c551f'. 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 b4cb2d4 automatic import of hmmer Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-raqbnmhq/hmmer rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading hmmer-3.3.2.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o hmmer-3.3.2.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/churchyard/setuptools-80.9.0:custom:isolated/hmmer/hmmer-3.3.2.tar.gz/md5/ea03d88b4e8228a1dc6d84d56af27195/hmmer-3.3.2.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 17.3M 100 17.3M 0 0 26.4M 0 --:--:-- --:--:-- --:--:-- 26.3M INFO: Reading stdout from command: md5sum hmmer-3.3.2.tar.gz tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-raqbnmhq/hmmer/hmmer.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-raqbnmhq/hmmer --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1759860757.492776 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.3 starting (python version = 3.13.7, NVR = mock-6.3-1.fc42), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-raqbnmhq/hmmer/hmmer.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-raqbnmhq/hmmer --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1759860757.492776 -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-raqbnmhq/hmmer/hmmer.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 6.3 INFO: Mock Version: 6.3 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1759860757.492776/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 container image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Tagging container image as mock-bootstrap-05722172-dec4-4f2a-a6a4-e3826888dc4e INFO: Checking that 28e0af93e676d22555d5249ba644149cac5818d6cfa18d6e38e7613a36536194 image matches host's architecture INFO: Copy content of container 28e0af93e676d22555d5249ba644149cac5818d6cfa18d6e38e7613a36536194 to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1759860757.492776/root INFO: mounting 28e0af93e676d22555d5249ba644149cac5818d6cfa18d6e38e7613a36536194 with podman image mount INFO: image 28e0af93e676d22555d5249ba644149cac5818d6cfa18d6e38e7613a36536194 as /var/lib/containers/storage/overlay/38801bbcb602df7f4f66ec64d423a1c11ef7d4c1b62e859f25b54dbbe408a634/merged INFO: umounting image 28e0af93e676d22555d5249ba644149cac5818d6cfa18d6e38e7613a36536194 (/var/lib/containers/storage/overlay/38801bbcb602df7f4f66ec64d423a1c11ef7d4c1b62e859f25b54dbbe408a634/merged) with podman image umount INFO: Removing image mock-bootstrap-05722172-dec4-4f2a-a6a4-e3826888dc4e 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-rawhide-x86_64-1759860757.492776/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-6.0.0-1.fc44.x86_64 rpm-sequoia-1.9.0-2.fc43.x86_64 dnf5-5.2.17.0-2.fc44.x86_64 dnf5-plugins-5.2.17.0-2.fc44.x86_64 Start: installing minimal buildroot with dnf5 Updating and loading repositories: Additional repo http_kojipkgs_fedorapr 100% | 58.0 KiB/s | 3.8 KiB | 00m00s Coprdir repository 100% | 23.3 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 23.0 KiB/s | 1.5 KiB | 00m00s fedora 100% | 182.0 KiB/s | 25.8 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash x86_64 5.3.0-2.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 8.4 MiB bzip2 x86_64 1.0.8-21.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 95.3 KiB coreutils x86_64 9.8-3.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 5.4 MiB cpio x86_64 2.15-6.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 1.1 MiB diffutils x86_64 3.12-3.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 1.6 MiB fedora-release-common noarch 44-0.4 copr_coprdir 20.6 KiB findutils x86_64 1:4.10.0-6.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 1.8 MiB gawk x86_64 5.3.2-2.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 1.8 MiB glibc-minimal-langpack x86_64 2.42.9000-5.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 0.0 B grep x86_64 3.12-2.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 1.0 MiB gzip x86_64 1.14-1.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 397.8 KiB info x86_64 7.2-6.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 353.9 KiB patch x86_64 2.8-2.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 222.8 KiB redhat-rpm-config noarch 343-14.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 183.3 KiB rpm-build x86_64 6.0.0-1.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 287.4 KiB sed x86_64 4.9-5.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 857.3 KiB shadow-utils x86_64 2:4.18.0-3.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 3.9 MiB tar x86_64 2:1.35-6.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 2.9 MiB unzip x86_64 6.0-68.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 390.3 KiB util-linux x86_64 2.41.1-17.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 3.5 MiB which x86_64 2.23-3.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 83.5 KiB xz x86_64 1:5.8.1-2.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 1.3 MiB Installing dependencies: add-determinism x86_64 0.7.2-2.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 2.3 MiB alternatives x86_64 1.33-2.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 62.2 KiB ansible-srpm-macros noarch 1-18.1.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 35.7 KiB audit-libs x86_64 4.1.2-2.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 378.8 KiB binutils x86_64 2.45.50-5.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 27.1 MiB build-reproducibility-srpm-macros noarch 0.7.2-2.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 1.2 KiB bzip2-libs x86_64 1.0.8-21.fc43 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http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 40.1 KiB elfutils x86_64 0.193-3.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 2.9 MiB elfutils-debuginfod-client x86_64 0.193-3.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 83.9 KiB elfutils-default-yama-scope noarch 0.193-3.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 1.8 KiB elfutils-libelf x86_64 0.193-3.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 1.2 MiB elfutils-libs x86_64 0.193-3.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 683.4 KiB fedora-gpg-keys noarch 44-0.1 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 131.2 KiB fedora-release noarch 44-0.4 copr_coprdir 0.0 B fedora-release-identity-basic noarch 44-0.4 copr_coprdir 664.0 B fedora-repos noarch 44-0.1 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 4.9 KiB fedora-repos-rawhide noarch 44-0.1 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 2.2 KiB file x86_64 5.46-8.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 100.2 KiB file-libs x86_64 5.46-8.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 11.9 MiB filesystem x86_64 3.18-50.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 112.0 B filesystem-srpm-macros noarch 3.18-50.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 38.2 KiB fonts-srpm-macros noarch 1:5.0.0-1.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 55.8 KiB forge-srpm-macros noarch 0.4.0-3.fc44 copr_coprdir 38.9 KiB fpc-srpm-macros noarch 1.3-15.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 144.0 B gap-srpm-macros noarch 2-1.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 2.1 KiB gdb-minimal x86_64 16.3-6.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 13.3 MiB gdbm-libs x86_64 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KiB gnupg2-gpgconf x86_64 2.4.8-4.fc44 copr_coprdir 250.0 KiB gnupg2-keyboxd x86_64 2.4.8-4.fc44 copr_coprdir 201.4 KiB gnupg2-verify x86_64 2.4.8-4.fc44 copr_coprdir 348.5 KiB gnutls x86_64 3.8.10-5.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 3.8 MiB go-srpm-macros noarch 3.8.0-1.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 61.9 KiB gpgverify noarch 2.2-3.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 8.7 KiB ima-evm-utils-libs x86_64 1.6.2-6.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 60.7 KiB jansson x86_64 2.14-3.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 89.1 KiB java-srpm-macros noarch 1-7.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 870.0 B json-c x86_64 0.18-7.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 82.7 KiB kernel-srpm-macros noarch 1.0-27.fc43 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http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 90.2 KiB xz-libs x86_64 1:5.8.1-2.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 217.8 KiB zig-srpm-macros noarch 1-5.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 1.1 KiB zip x86_64 3.0-44.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 694.5 KiB zlib-ng-compat x86_64 2.2.5-2.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 137.6 KiB zstd x86_64 1.5.7-3.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 506.2 KiB Installing groups: Buildsystem building group Transaction Summary: Installing: 177 packages Total size of inbound packages is 66 MiB. 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| 00m00s >>> Running %pretrans scriptlet: filesystem-0:3.18-50.fc43.x86_64 >>> Finished %pretrans scriptlet: filesystem-0:3.18-50.fc43.x86_64 >>> [RPM] /var/lib/mock/fedora-rawhide-x86_64-1759860757.492776/root/var/cache/d [ 2/179] Prepare transaction 100% | 3.3 KiB/s | 177.0 B | 00m00s [ 3/179] Installing libgcc-0:15.2.1-2. 100% | 262.0 MiB/s | 268.3 KiB | 00m00s [ 4/179] Installing publicsuffix-list- 100% | 0.0 B/s | 69.8 KiB | 00m00s [ 5/179] Installing libssh-config-0:0. 100% | 0.0 B/s | 816.0 B | 00m00s [ 6/179] Installing fedora-release-ide 100% | 0.0 B/s | 920.0 B | 00m00s [ 7/179] Installing fedora-gpg-keys-0: 100% | 43.7 MiB/s | 179.0 KiB | 00m00s [ 8/179] Installing fedora-repos-rawhi 100% | 0.0 B/s | 2.4 KiB | 00m00s [ 9/179] Installing fedora-repos-0:44- 100% | 0.0 B/s | 5.7 KiB | 00m00s [ 10/179] Installing fedora-release-com 100% | 24.3 MiB/s | 24.9 KiB | 00m00s [ 11/179] Installing fedora-release-0:4 100% | 17.3 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.0-26.fc43.noarch >>> Finished sysusers scriptlet: setup-0:2.15.0-26.fc43.noarch >>> Scriptlet output: >>> Creating group 'adm' with GID 4. >>> Creating group 'audio' with GID 63. >>> Creating group 'cdrom' with GID 11. >>> Creating group 'clock' with GID 103. >>> Creating group 'dialout' with GID 18. >>> Creating group 'disk' with GID 6. >>> Creating group 'floppy' with GID 19. >>> Creating group 'ftp' with GID 50. >>> Creating group 'games' with GID 20. >>> Creating group 'input' with GID 104. >>> Creating group 'kmem' with GID 9. >>> Creating group 'kvm' with GID 36. >>> Creating group 'lock' with GID 54. >>> Creating group 'lp' with GID 7. >>> Creating group 'mail' with GID 12. >>> Creating group 'man' with GID 15. >>> Creating group 'mem' with GID 8. >>> Creating group 'nobody' with GID 65534. >>> Creating group 'render' with GID 105. >>> Creating group 'root' with GID 0. >>> Creating group 'sgx' with GID 106. >>> Creating group 'sys' with GID 3. >>> Creating group 'tape' with GID 33. >>> Creating group 'tty' with GID 5. >>> Creating group 'users' with GID 100. >>> Creating group 'utmp' with GID 22. >>> Creating group 'video' with GID 39. >>> Creating group 'wheel' with GID 10. >>> Creating user 'adm' (adm) with UID 3 and GID 4. >>> Creating group 'bin' with GID 1. >>> Creating user 'bin' (bin) with UID 1 and GID 1. >>> Creating group 'daemon' with GID 2. >>> Creating user 'daemon' (daemon) with UID 2 and GID 2. >>> Creating user 'ftp' (FTP User) with UID 14 and GID 50. >>> Creating user 'games' (games) with UID 12 and GID 100. >>> Creating user 'halt' (halt) with UID 7 and GID 0. >>> Creating user 'lp' (lp) with UID 4 and GID 7. >>> Creating user 'mail' (mail) with UID 8 and GID 12. >>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534. >>> Creating user 'operator' (operator) with UID 11 and GID 0. >>> Creating user 'root' (Super User) with UID 0 and GID 0. >>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0. >>> Creating user 'sync' (sync) with UID 5 and GID 0. >>> [ 12/179] Installing setup-0:2.15.0-26. 100% | 54.9 MiB/s | 730.6 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 13/179] Installing filesystem-0:3.18- 100% | 2.8 MiB/s | 212.8 KiB | 00m00s [ 14/179] Installing gnulib-l10n-0:2024 100% | 215.5 MiB/s | 661.9 KiB | 00m00s [ 15/179] Installing coreutils-common-0 100% | 399.1 MiB/s | 11.2 MiB | 00m00s [ 16/179] Installing pcre2-syntax-0:10. 100% | 271.2 MiB/s | 277.8 KiB | 00m00s [ 17/179] Installing ncurses-base-0:6.5 100% | 86.3 MiB/s | 353.5 KiB | 00m00s [ 18/179] Installing bash-0:5.3.0-2.fc4 100% | 290.7 MiB/s | 8.4 MiB | 00m00s [ 19/179] Installing glibc-common-0:2.4 100% | 72.9 MiB/s | 1.0 MiB | 00m00s [ 20/179] Installing glibc-gconv-extra- 100% | 292.4 MiB/s | 7.3 MiB | 00m00s [ 21/179] Installing glibc-0:2.42.9000- 100% | 191.4 MiB/s | 6.7 MiB | 00m00s [ 22/179] Installing ncurses-libs-0:6.5 100% | 310.1 MiB/s | 952.8 KiB | 00m00s [ 23/179] Installing glibc-minimal-lang 100% | 0.0 B/s | 124.0 B | 00m00s [ 24/179] Installing zlib-ng-compat-0:2 100% | 135.2 MiB/s | 138.4 KiB | 00m00s [ 25/179] Installing bzip2-libs-0:1.0.8 100% | 0.0 B/s | 81.7 KiB | 00m00s [ 26/179] Installing libgpg-error-0:1.5 100% | 69.2 MiB/s | 921.1 KiB | 00m00s [ 27/179] Installing libstdc++-0:15.2.1 100% | 406.3 MiB/s | 2.8 MiB | 00m00s [ 28/179] Installing libassuan-0:2.5.7- 100% | 161.7 MiB/s | 165.6 KiB | 00m00s [ 29/179] Installing libgcrypt-0:1.11.1 100% | 393.8 MiB/s | 1.6 MiB | 00m00s [ 30/179] Installing readline-0:8.3-2.f 100% | 250.9 MiB/s | 513.9 KiB | 00m00s [ 31/179] Installing xz-libs-1:5.8.1-2. 100% | 213.8 MiB/s | 218.9 KiB | 00m00s [ 32/179] Installing libuuid-0:2.41.1-1 100% | 0.0 B/s | 38.5 KiB | 00m00s [ 33/179] Installing gmp-1:6.3.0-4.fc44 100% | 399.2 MiB/s | 817.5 KiB | 00m00s [ 34/179] Installing popt-0:1.19-9.fc43 100% | 68.1 MiB/s | 139.4 KiB | 00m00s [ 35/179] Installing libzstd-0:1.5.7-3. 100% | 459.7 MiB/s | 941.6 KiB | 00m00s [ 36/179] Installing elfutils-libelf-0: 100% | 388.8 MiB/s | 1.2 MiB | 00m00s [ 37/179] Installing npth-0:1.8-3.fc43. 100% | 0.0 B/s | 50.7 KiB | 00m00s [ 38/179] Installing libblkid-0:2.41.1- 100% | 257.3 MiB/s | 263.5 KiB | 00m00s [ 39/179] Installing libxcrypt-0:4.4.38 100% | 280.4 MiB/s | 287.1 KiB | 00m00s [ 40/179] Installing libsepol-0:3.9-2.f 100% | 401.8 MiB/s | 822.9 KiB | 00m00s [ 41/179] Installing sqlite-libs-0:3.50 100% | 379.1 MiB/s | 1.5 MiB | 00m00s [ 42/179] Installing gnupg2-gpgconf-0:2 100% | 20.5 MiB/s | 252.1 KiB | 00m00s [ 43/179] Installing libattr-0:2.5.2-6. 100% | 0.0 B/s | 25.4 KiB | 00m00s [ 44/179] Installing libacl-0:2.3.2-4.f 100% | 0.0 B/s | 36.8 KiB | 00m00s [ 45/179] Installing pcre2-0:10.46-1.fc 100% | 341.4 MiB/s | 699.1 KiB | 00m00s [ 46/179] Installing libselinux-0:3.9-5 100% | 189.8 MiB/s | 194.4 KiB | 00m00s [ 47/179] Installing grep-0:3.12-2.fc43 100% | 71.6 MiB/s | 1.0 MiB | 00m00s [ 48/179] Installing sed-0:4.9-5.fc43.x 100% | 60.4 MiB/s | 865.5 KiB | 00m00s [ 49/179] Installing findutils-1:4.10.0 100% | 116.1 MiB/s | 1.9 MiB | 00m00s [ 50/179] Installing libtasn1-0:4.20.0- 100% | 173.9 MiB/s | 178.1 KiB | 00m00s [ 51/179] Installing libunistring-0:1.1 100% | 431.7 MiB/s | 1.7 MiB | 00m00s [ 52/179] Installing libidn2-0:2.3.8-2. 100% | 60.6 MiB/s | 558.7 KiB | 00m00s [ 53/179] Installing crypto-policies-0: 100% | 42.0 MiB/s | 172.0 KiB | 00m00s [ 54/179] Installing xz-1:5.8.1-2.fc43. 100% | 78.3 MiB/s | 1.3 MiB | 00m00s [ 55/179] Installing libmount-0:2.41.1- 100% | 365.0 MiB/s | 373.8 KiB | 00m00s [ 56/179] Installing gnupg2-verify-0:2. 100% | 31.0 MiB/s | 349.7 KiB | 00m00s [ 57/179] Installing dwz-0:0.16-2.fc43. 100% | 25.6 MiB/s | 288.5 KiB | 00m00s [ 58/179] Installing mpfr-0:4.2.2-2.fc4 100% | 407.4 MiB/s | 834.4 KiB | 00m00s [ 59/179] Installing gawk-0:5.3.2-2.fc4 100% | 113.5 MiB/s | 1.8 MiB | 00m00s [ 60/179] Installing libksba-0:1.6.7-4. 100% | 391.7 MiB/s | 401.1 KiB | 00m00s [ 61/179] Installing unzip-0:6.0-68.fc4 100% | 35.0 MiB/s | 393.8 KiB | 00m00s [ 62/179] Installing file-libs-0:5.46-8 100% | 697.5 MiB/s | 11.9 MiB | 00m00s [ 63/179] Installing file-0:5.46-8.fc44 100% | 9.0 MiB/s | 101.7 KiB | 00m00s [ 64/179] Installing diffutils-0:3.12-3 100% | 104.1 MiB/s | 1.6 MiB | 00m00s [ 65/179] Installing libcap-ng-0:0.8.5- 100% | 0.0 B/s | 70.8 KiB | 00m00s [ 66/179] Installing audit-libs-0:4.1.2 100% | 372.6 MiB/s | 381.5 KiB | 00m00s [ 67/179] Installing libsemanage-0:3.9- 100% | 303.0 MiB/s | 310.2 KiB | 00m00s [ 68/179] Installing libsmartcols-0:2.4 100% | 177.3 MiB/s | 181.6 KiB | 00m00s [ 69/179] Installing libeconf-0:0.7.9-2 100% | 0.0 B/s | 66.5 KiB | 00m00s [ 70/179] Installing pam-libs-0:1.7.1-3 100% | 126.0 MiB/s | 129.0 KiB | 00m00s [ 71/179] Installing libcap-0:2.76-3.fc 100% | 17.4 MiB/s | 214.3 KiB | 00m00s [ 72/179] Installing systemd-libs-0:258 100% | 387.5 MiB/s | 2.3 MiB | 00m00s [ 73/179] Installing alternatives-0:1.3 100% | 6.2 MiB/s | 63.8 KiB | 00m00s [ 74/179] Installing lua-libs-0:5.4.8-2 100% | 275.3 MiB/s | 281.9 KiB | 00m00s [ 75/179] Installing json-c-0:0.18-7.fc 100% | 0.0 B/s | 84.0 KiB | 00m00s [ 76/179] Installing libffi-0:3.5.2-1.f 100% | 83.2 MiB/s | 85.2 KiB | 00m00s [ 77/179] Installing p11-kit-0:0.25.8-1 100% | 127.2 MiB/s | 2.3 MiB | 00m00s [ 78/179] Installing p11-kit-trust-0:0. 100% | 23.0 MiB/s | 448.3 KiB | 00m00s [ 79/179] Installing openssl-libs-1:3.5 100% | 400.9 MiB/s | 9.2 MiB | 00m00s [ 80/179] Installing coreutils-0:9.8-3. 100% | 171.1 MiB/s | 5.5 MiB | 00m00s [ 81/179] Installing ca-certificates-0: 100% | 2.1 MiB/s | 2.5 MiB | 00m01s [ 82/179] Installing gzip-0:1.14-1.fc44 100% | 30.3 MiB/s | 403.3 KiB | 00m00s [ 83/179] Installing rpm-sequoia-0:1.9. 100% | 354.1 MiB/s | 2.5 MiB | 00m00s [ 84/179] Installing libfsverity-0:1.6- 100% | 0.0 B/s | 29.5 KiB | 00m00s [ 85/179] Installing libevent-0:2.1.12- 100% | 288.7 MiB/s | 886.8 KiB | 00m00s [ 86/179] Installing util-linux-core-0: 100% | 92.5 MiB/s | 1.5 MiB | 00m00s [ 87/179] Installing libusb1-0:1.0.29-4 100% | 21.1 MiB/s | 172.9 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.x86_64 >>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.x86_64 >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [ 88/179] Installing tpm2-tss-0:4.1.3-8 100% | 262.0 MiB/s | 1.6 MiB | 00m00s [ 89/179] Installing gnupg2-gpg-agent-0 100% | 34.7 MiB/s | 675.4 KiB | 00m00s [ 90/179] Installing ima-evm-utils-libs 100% | 60.5 MiB/s | 62.0 KiB | 00m00s [ 91/179] Installing systemd-standalone 100% | 23.9 MiB/s | 294.1 KiB | 00m00s [ 92/179] Installing rpm-libs-0:6.0.0-1 100% | 304.5 MiB/s | 935.3 KiB | 00m00s [ 93/179] Installing zip-0:3.0-44.fc43. 100% | 52.5 MiB/s | 698.4 KiB | 00m00s [ 94/179] Installing gnupg2-keyboxd-0:2 100% | 33.0 MiB/s | 202.7 KiB | 00m00s [ 95/179] Installing libpsl-0:0.21.5-6. 100% | 75.7 MiB/s | 77.5 KiB | 00m00s [ 96/179] Installing tar-2:1.35-6.fc43. 100% | 155.7 MiB/s | 3.0 MiB | 00m00s [ 97/179] Installing linkdupes-0:0.7.2- 100% | 63.1 MiB/s | 840.1 KiB | 00m00s [ 98/179] Installing libselinux-utils-0 100% | 24.3 MiB/s | 323.4 KiB | 00m00s [ 99/179] Installing liblastlog2-0:2.41 100% | 5.8 MiB/s | 35.9 KiB | 00m00s [100/179] Installing libfdisk-0:2.41.1- 100% | 186.2 MiB/s | 381.4 KiB | 00m00s [101/179] Installing util-linux-0:2.41. 100% | 105.1 MiB/s | 3.6 MiB | 00m00s [102/179] Installing policycoreutils-0: 100% | 30.2 MiB/s | 711.8 KiB | 00m00s [103/179] Installing selinux-policy-0:4 100% | 1.8 MiB/s | 33.5 KiB | 00m00s [104/179] Installing selinux-policy-tar 100% | 196.0 MiB/s | 14.9 MiB | 00m00s [105/179] Installing zstd-0:1.5.7-3.fc4 100% | 33.2 MiB/s | 509.8 KiB | 00m00s [106/179] Installing nettle-0:3.10.1-2. 100% | 258.4 MiB/s | 793.7 KiB | 00m00s [107/179] Installing gnutls-0:3.8.10-5. 100% | 384.3 MiB/s | 3.8 MiB | 00m00s [108/179] Installing libxml2-0:2.12.10- 100% | 106.5 MiB/s | 1.7 MiB | 00m00s [109/179] Installing bzip2-0:1.0.8-21.f 100% | 8.1 MiB/s | 99.8 KiB | 00m00s [110/179] Installing add-determinism-0: 100% | 144.1 MiB/s | 2.3 MiB | 00m00s [111/179] Installing build-reproducibil 100% | 0.0 B/s | 1.5 KiB | 00m00s [112/179] Installing cpio-0:2.15-6.fc43 100% | 78.5 MiB/s | 1.1 MiB | 00m00s [113/179] Installing libpkgconf-0:2.3.0 100% | 77.4 MiB/s | 79.2 KiB | 00m00s [114/179] Installing pkgconf-0:2.3.0-3. 100% | 8.1 MiB/s | 91.0 KiB | 00m00s [115/179] Installing ed-0:1.22.2-1.fc44 100% | 13.3 MiB/s | 150.4 KiB | 00m00s [116/179] Installing patch-0:2.8-2.fc43 100% | 19.9 MiB/s | 224.3 KiB | 00m00s [117/179] Installing lz4-libs-0:1.10.0- 100% | 158.6 MiB/s | 162.5 KiB | 00m00s [118/179] Installing libarchive-0:3.8.1 100% | 310.2 MiB/s | 953.1 KiB | 00m00s [119/179] Installing jansson-0:2.14-3.f 100% | 88.3 MiB/s | 90.5 KiB | 00m00s [120/179] Installing libgomp-0:15.2.1-2 100% | 264.9 MiB/s | 542.5 KiB | 00m00s [121/179] Installing libtool-ltdl-0:2.5 100% | 0.0 B/s | 71.2 KiB | 00m00s [122/179] Installing gdbm-libs-1:1.23-1 100% | 128.5 MiB/s | 131.6 KiB | 00m00s [123/179] Installing cyrus-sasl-lib-0:2 100% | 135.3 MiB/s | 2.3 MiB | 00m00s [124/179] Installing openldap-0:2.6.10- 100% | 216.0 MiB/s | 663.6 KiB | 00m00s [125/179] Installing gnupg2-dirmngr-0:2 100% | 30.3 MiB/s | 621.1 KiB | 00m00s [126/179] Installing gnupg2-0:2.4.8-4.f 100% | 223.0 MiB/s | 6.5 MiB | 00m00s [127/179] Installing rpm-sign-libs-0:6. 100% | 39.6 MiB/s | 40.6 KiB | 00m00s [128/179] Installing gpgverify-0:2.2-3. 100% | 0.0 B/s | 9.4 KiB | 00m00s [129/179] Installing xxhash-libs-0:0.8. 100% | 89.4 MiB/s | 91.6 KiB | 00m00s [130/179] Installing libbrotli-0:1.1.0- 100% | 272.0 MiB/s | 835.6 KiB | 00m00s [131/179] Installing libnghttp2-0:1.67. 100% | 159.5 MiB/s | 163.4 KiB | 00m00s [132/179] Installing keyutils-libs-0:1. 100% | 54.4 MiB/s | 55.7 KiB | 00m00s [133/179] Installing libcom_err-0:1.47. 100% | 0.0 B/s | 64.2 KiB | 00m00s [134/179] Installing libverto-0:0.3.2-1 100% | 26.6 MiB/s | 27.2 KiB | 00m00s [135/179] Installing krb5-libs-0:1.21.3 100% | 328.5 MiB/s | 2.3 MiB | 00m00s [136/179] Installing libssh-0:0.11.3-1. 100% | 277.9 MiB/s | 569.2 KiB | 00m00s [137/179] Installing libcurl-0:8.16.0-1 100% | 299.7 MiB/s | 920.6 KiB | 00m00s [138/179] Installing curl-0:8.16.0-1.fc 100% | 21.2 MiB/s | 478.1 KiB | 00m00s [139/179] Installing rpm-0:6.0.0-1.fc44 100% | 78.0 MiB/s | 2.6 MiB | 00m00s [140/179] Installing efi-srpm-macros-0: 100% | 40.2 MiB/s | 41.1 KiB | 00m00s [141/179] Installing java-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [142/179] Installing lua-srpm-macros-0: 100% | 0.0 B/s | 1.9 KiB | 00m00s [143/179] Installing tree-sitter-srpm-m 100% | 0.0 B/s | 9.3 KiB | 00m00s [144/179] Installing zig-srpm-macros-0: 100% | 0.0 B/s | 1.7 KiB | 00m00s [145/179] Installing filesystem-srpm-ma 100% | 0.0 B/s | 38.9 KiB | 00m00s [146/179] Installing elfutils-default-y 100% | 408.6 KiB/s | 2.0 KiB | 00m00s [147/179] Installing elfutils-libs-0:0. 100% | 223.1 MiB/s | 685.2 KiB | 00m00s [148/179] Installing elfutils-debuginfo 100% | 6.5 MiB/s | 86.2 KiB | 00m00s [149/179] Installing binutils-0:2.45.50 100% | 326.8 MiB/s | 27.1 MiB | 00m00s [150/179] Installing elfutils-0:0.193-3 100% | 153.6 MiB/s | 2.9 MiB | 00m00s [151/179] Installing gdb-minimal-0:16.3 100% | 301.3 MiB/s | 13.3 MiB | 00m00s [152/179] Installing debugedit-0:5.2-3. 100% | 17.7 MiB/s | 217.3 KiB | 00m00s [153/179] Installing rpm-build-libs-0:6 100% | 262.9 MiB/s | 269.2 KiB | 00m00s [154/179] Installing pkgconf-m4-0:2.3.0 100% | 0.0 B/s | 14.8 KiB | 00m00s [155/179] Installing pkgconf-pkg-config 100% | 161.2 KiB/s | 1.8 KiB | 00m00s [156/179] Installing rust-srpm-macros-0 100% | 0.0 B/s | 5.6 KiB | 00m00s [157/179] Installing qt6-srpm-macros-0: 100% | 0.0 B/s | 740.0 B | 00m00s [158/179] Installing qt5-srpm-macros-0: 100% | 0.0 B/s | 776.0 B | 00m00s [159/179] Installing perl-srpm-macros-0 100% | 0.0 B/s | 1.1 KiB | 00m00s [160/179] Installing package-notes-srpm 100% | 0.0 B/s | 2.0 KiB | 00m00s [161/179] Installing openblas-srpm-macr 100% | 0.0 B/s | 392.0 B | 00m00s [162/179] Installing ocaml-srpm-macros- 100% | 0.0 B/s | 2.1 KiB | 00m00s [163/179] Installing kernel-srpm-macros 100% | 0.0 B/s | 2.3 KiB | 00m00s [164/179] Installing gnat-srpm-macros-0 100% | 0.0 B/s | 1.3 KiB | 00m00s [165/179] Installing ghc-srpm-macros-0: 100% | 0.0 B/s | 1.0 KiB | 00m00s [166/179] Installing gap-srpm-macros-0: 100% | 0.0 B/s | 2.7 KiB | 00m00s [167/179] Installing fpc-srpm-macros-0: 100% | 0.0 B/s | 420.0 B | 00m00s [168/179] Installing ansible-srpm-macro 100% | 0.0 B/s | 36.2 KiB | 00m00s [169/179] Installing rpm-build-0:6.0.0- 100% | 22.3 MiB/s | 296.5 KiB | 00m00s [170/179] Installing pyproject-srpm-mac 100% | 0.0 B/s | 2.5 KiB | 00m00s [171/179] Installing redhat-rpm-config- 100% | 92.5 MiB/s | 189.5 KiB | 00m00s [172/179] Installing forge-srpm-macros- 100% | 0.0 B/s | 40.3 KiB | 00m00s [173/179] Installing fonts-srpm-macros- 100% | 0.0 B/s | 57.0 KiB | 00m00s [174/179] Installing go-srpm-macros-0:3 100% | 0.0 B/s | 63.0 KiB | 00m00s [175/179] Installing python-srpm-macros 100% | 0.0 B/s | 52.9 KiB | 00m00s [176/179] Installing rpm-plugin-selinux 100% | 0.0 B/s | 13.0 KiB | 00m00s [177/179] Installing which-0:2.23-3.fc4 100% | 7.0 MiB/s | 85.7 KiB | 00m00s [178/179] Installing shadow-utils-2:4.1 100% | 128.0 MiB/s | 4.0 MiB | 00m00s [179/179] Installing info-0:7.2-6.fc43. 100% | 46.2 KiB/s | 354.3 KiB | 00m08s Warning: skipped OpenPGP checks for 177 packages from repositories: copr_coprdir, http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: add-determinism-0.7.2-2.fc44.x86_64 alternatives-1.33-2.fc43.x86_64 ansible-srpm-macros-1-18.1.fc43.noarch audit-libs-4.1.2-2.fc44.x86_64 bash-5.3.0-2.fc43.x86_64 binutils-2.45.50-5.fc44.x86_64 build-reproducibility-srpm-macros-0.7.2-2.fc44.noarch bzip2-1.0.8-21.fc43.x86_64 bzip2-libs-1.0.8-21.fc43.x86_64 ca-certificates-2025.2.80_v9.0.304-2.fc44.noarch coreutils-9.8-3.fc44.x86_64 coreutils-common-9.8-3.fc44.x86_64 cpio-2.15-6.fc43.x86_64 crypto-policies-20250714-5.gitcd6043a.fc44.noarch curl-8.16.0-1.fc44.x86_64 cyrus-sasl-lib-2.1.28-33.fc44.x86_64 debugedit-5.2-3.fc44.x86_64 diffutils-3.12-3.fc43.x86_64 dwz-0.16-2.fc43.x86_64 ed-1.22.2-1.fc44.x86_64 efi-srpm-macros-6-4.fc43.noarch elfutils-0.193-3.fc43.x86_64 elfutils-debuginfod-client-0.193-3.fc43.x86_64 elfutils-default-yama-scope-0.193-3.fc43.noarch elfutils-libelf-0.193-3.fc43.x86_64 elfutils-libs-0.193-3.fc43.x86_64 fedora-gpg-keys-44-0.1.noarch fedora-release-44-0.4.noarch fedora-release-common-44-0.4.noarch fedora-release-identity-basic-44-0.4.noarch fedora-repos-44-0.1.noarch fedora-repos-rawhide-44-0.1.noarch file-5.46-8.fc44.x86_64 file-libs-5.46-8.fc44.x86_64 filesystem-3.18-50.fc43.x86_64 filesystem-srpm-macros-3.18-50.fc43.noarch findutils-4.10.0-6.fc43.x86_64 fonts-srpm-macros-5.0.0-1.fc44.noarch forge-srpm-macros-0.4.0-3.fc44.noarch fpc-srpm-macros-1.3-15.fc43.noarch gap-srpm-macros-2-1.fc44.noarch gawk-5.3.2-2.fc43.x86_64 gdb-minimal-16.3-6.fc44.x86_64 gdbm-libs-1.23-10.fc43.x86_64 ghc-srpm-macros-1.9.2-3.fc43.noarch glibc-2.42.9000-5.fc44.x86_64 glibc-common-2.42.9000-5.fc44.x86_64 glibc-gconv-extra-2.42.9000-5.fc44.x86_64 glibc-minimal-langpack-2.42.9000-5.fc44.x86_64 gmp-6.3.0-4.fc44.x86_64 gnat-srpm-macros-6-8.fc43.noarch gnulib-l10n-20241231-1.fc44.noarch gnupg2-2.4.8-4.fc44.x86_64 gnupg2-dirmngr-2.4.8-4.fc44.x86_64 gnupg2-gpg-agent-2.4.8-4.fc44.x86_64 gnupg2-gpgconf-2.4.8-4.fc44.x86_64 gnupg2-keyboxd-2.4.8-4.fc44.x86_64 gnupg2-verify-2.4.8-4.fc44.x86_64 gnutls-3.8.10-5.fc44.x86_64 go-srpm-macros-3.8.0-1.fc44.noarch gpgverify-2.2-3.fc43.noarch grep-3.12-2.fc43.x86_64 gzip-1.14-1.fc44.x86_64 ima-evm-utils-libs-1.6.2-6.fc43.x86_64 info-7.2-6.fc43.x86_64 jansson-2.14-3.fc43.x86_64 java-srpm-macros-1-7.fc43.noarch json-c-0.18-7.fc43.x86_64 kernel-srpm-macros-1.0-27.fc43.noarch keyutils-libs-1.6.3-6.fc43.x86_64 krb5-libs-1.21.3-8.fc44.x86_64 libacl-2.3.2-4.fc43.x86_64 libarchive-3.8.1-3.fc43.x86_64 libassuan-2.5.7-4.fc43.x86_64 libattr-2.5.2-6.fc43.x86_64 libblkid-2.41.1-17.fc44.x86_64 libbrotli-1.1.0-10.fc44.x86_64 libcap-2.76-3.fc44.x86_64 libcap-ng-0.8.5-8.fc44.x86_64 libcom_err-1.47.3-2.fc44.x86_64 libcurl-8.16.0-1.fc44.x86_64 libeconf-0.7.9-2.fc43.x86_64 libevent-2.1.12-16.fc43.x86_64 libfdisk-2.41.1-17.fc44.x86_64 libffi-3.5.2-1.fc44.x86_64 libfsverity-1.6-3.fc43.x86_64 libgcc-15.2.1-2.fc44.x86_64 libgcrypt-1.11.1-2.fc43.x86_64 libgomp-15.2.1-2.fc44.x86_64 libgpg-error-1.55-2.fc43.x86_64 libidn2-2.3.8-2.fc43.x86_64 libksba-1.6.7-4.fc43.x86_64 liblastlog2-2.41.1-17.fc44.x86_64 libmount-2.41.1-17.fc44.x86_64 libnghttp2-1.67.1-1.fc44.x86_64 libpkgconf-2.3.0-3.fc43.x86_64 libpsl-0.21.5-6.fc43.x86_64 libselinux-3.9-5.fc44.x86_64 libselinux-utils-3.9-5.fc44.x86_64 libsemanage-3.9-4.fc44.x86_64 libsepol-3.9-2.fc43.x86_64 libsmartcols-2.41.1-17.fc44.x86_64 libssh-0.11.3-1.fc44.x86_64 libssh-config-0.11.3-1.fc44.noarch libstdc++-15.2.1-2.fc44.x86_64 libtasn1-4.20.0-2.fc43.x86_64 libtool-ltdl-2.5.4-7.fc43.x86_64 libunistring-1.1-10.fc43.x86_64 libusb1-1.0.29-4.fc44.x86_64 libuuid-2.41.1-17.fc44.x86_64 libverto-0.3.2-11.fc43.x86_64 libxcrypt-4.4.38-9.fc44.x86_64 libxml2-2.12.10-5.fc44.x86_64 libzstd-1.5.7-3.fc44.x86_64 linkdupes-0.7.2-2.fc44.x86_64 lua-libs-5.4.8-2.fc43.x86_64 lua-srpm-macros-1-16.fc43.noarch lz4-libs-1.10.0-3.fc43.x86_64 mpfr-4.2.2-2.fc43.x86_64 ncurses-base-6.5-7.20250614.fc43.noarch ncurses-libs-6.5-7.20250614.fc43.x86_64 nettle-3.10.1-2.fc43.x86_64 npth-1.8-3.fc43.x86_64 ocaml-srpm-macros-11-2.fc43.noarch openblas-srpm-macros-2-20.fc43.noarch openldap-2.6.10-4.fc44.x86_64 openssl-libs-3.5.1-3.fc44.x86_64 p11-kit-0.25.8-1.fc44.x86_64 p11-kit-trust-0.25.8-1.fc44.x86_64 package-notes-srpm-macros-0.5-14.fc43.noarch pam-libs-1.7.1-3.fc43.x86_64 patch-2.8-2.fc43.x86_64 pcre2-10.46-1.fc44.x86_64 pcre2-syntax-10.46-1.fc44.noarch perl-srpm-macros-1-60.fc43.noarch pkgconf-2.3.0-3.fc43.x86_64 pkgconf-m4-2.3.0-3.fc43.noarch pkgconf-pkg-config-2.3.0-3.fc43.x86_64 policycoreutils-3.9-5.fc44.x86_64 popt-1.19-9.fc43.x86_64 publicsuffix-list-dafsa-20250616-2.fc43.noarch pyproject-srpm-macros-1.18.4-1.fc44.noarch python-srpm-macros-3.14-8.fc44.noarch qt5-srpm-macros-5.15.17-2.fc43.noarch qt6-srpm-macros-6.10.0~rc-1.fc44.noarch readline-8.3-2.fc43.x86_64 redhat-rpm-config-343-14.fc44.noarch rpm-6.0.0-1.fc44.x86_64 rpm-build-6.0.0-1.fc44.x86_64 rpm-build-libs-6.0.0-1.fc44.x86_64 rpm-libs-6.0.0-1.fc44.x86_64 rpm-plugin-selinux-6.0.0-1.fc44.x86_64 rpm-sequoia-1.9.0-2.fc43.x86_64 rpm-sign-libs-6.0.0-1.fc44.x86_64 rust-srpm-macros-26.4-1.fc44.noarch sed-4.9-5.fc43.x86_64 selinux-policy-42.12-1.fc44.noarch selinux-policy-targeted-42.12-1.fc44.noarch setup-2.15.0-26.fc43.noarch shadow-utils-4.18.0-3.fc43.x86_64 sqlite-libs-3.50.4-1.fc44.x86_64 systemd-libs-258-1.fc44.x86_64 systemd-standalone-sysusers-258-1.fc44.x86_64 tar-1.35-6.fc43.x86_64 tpm2-tss-4.1.3-8.fc43.x86_64 tree-sitter-srpm-macros-0.4.2-1.fc43.noarch unzip-6.0-68.fc44.x86_64 util-linux-2.41.1-17.fc44.x86_64 util-linux-core-2.41.1-17.fc44.x86_64 which-2.23-3.fc43.x86_64 xxhash-libs-0.8.3-3.fc43.x86_64 xz-5.8.1-2.fc43.x86_64 xz-libs-5.8.1-2.fc43.x86_64 zig-srpm-macros-1-5.fc43.noarch zip-3.0-44.fc43.x86_64 zlib-ng-compat-2.2.5-2.fc44.x86_64 zstd-1.5.7-3.fc44.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1753315200 Wrote: /builddir/build/SRPMS/hmmer-3.3.2-11.fc44.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1759860757.492776/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-raqbnmhq/hmmer/hmmer.spec) Config(child) 0 minutes 20 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/hmmer-3.3.2-11.fc44.src.rpm) Config(fedora-rawhide-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1759860757.492776/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1759860757.492776/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-rawhide-x86_64-1759860757.492776/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-6.0.0-1.fc44.x86_64 rpm-sequoia-1.9.0-2.fc43.x86_64 dnf5-5.2.17.0-2.fc44.x86_64 dnf5-plugins-5.2.17.0-2.fc44.x86_64 Finish: chroot init Start: build phase for hmmer-3.3.2-11.fc44.src.rpm Start: build setup for hmmer-3.3.2-11.fc44.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1753315200 Wrote: /builddir/build/SRPMS/hmmer-3.3.2-11.fc44.src.rpm Updating and loading repositories: Additional repo http_kojipkgs_fedorapr 100% | 47.3 KiB/s | 3.8 KiB | 00m00s Coprdir repository 100% | 19.0 KiB/s | 1.5 KiB | 00m00s Copr repository 100% | 18.7 KiB/s | 1.5 KiB | 00m00s fedora 100% | 71.6 KiB/s | 25.8 KiB | 00m00s Repositories loaded. 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http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 6.1 KiB perl-macros noarch 4:5.42.0-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 5.5 KiB perl-meta-notation noarch 5.42.0-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 2.0 KiB perl-mro x86_64 1.29-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 41.6 KiB perl-open noarch 1.13-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 11.3 KiB perl-overload noarch 1.40-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 71.6 KiB perl-overloading noarch 0.02-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 4.9 KiB perl-parent noarch 1:0.244-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 10.3 KiB perl-perlfaq noarch 5.20250619-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 733.6 KiB perl-ph x86_64 5.42.0-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 276.4 KiB perl-podlators noarch 1:6.0.2-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 317.5 KiB perl-sigtrap noarch 1.10-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 11.1 KiB perl-sort noarch 2.06-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 4.8 KiB perl-subs noarch 1.04-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 2.1 KiB perl-threads x86_64 1:2.43-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 115.1 KiB perl-threads-shared x86_64 1.70-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 83.6 KiB perl-utils noarch 5.42.0-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 97.0 KiB perl-vars noarch 1.05-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 3.9 KiB perl-version x86_64 9:0.99.33-521.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 128.7 KiB perl-vmsish noarch 1.04-520.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 6.6 KiB python-pip-wheel noarch 25.2-4.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 1.2 MiB python3 x86_64 3.14.0~rc3-1.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 28.9 KiB python3-libs x86_64 3.14.0~rc3-1.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 43.0 MiB python3-pyparsing noarch 3.1.2-14.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 1.0 MiB systemtap-sdt-devel x86_64 5.4~pre17585496g86ab88eb-1.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 183.7 KiB systemtap-sdt-dtrace x86_64 5.4~pre17585496g86ab88eb-1.fc44 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 180.3 KiB tzdata noarch 2025b-3.fc43 http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch 1.6 MiB Transaction Summary: Installing: 240 packages Total size of inbound packages is 112 MiB. Need to download 13 MiB. After this operation, 358 MiB extra will be used (install 358 MiB, remove 0 B). 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117.6 MiB/s | 120.4 KiB | 00m00s [219/242] Installing perl-Algorithm-Dif 100% | 106.9 MiB/s | 109.5 KiB | 00m00s [220/242] Installing perl-Text-Diff-0:1 100% | 83.1 MiB/s | 85.1 KiB | 00m00s [221/242] Installing perl-Module-Signat 100% | 11.3 MiB/s | 138.8 KiB | 00m00s [222/242] Installing perl-Compress-Raw- 100% | 120.4 MiB/s | 123.3 KiB | 00m00s [223/242] Installing perl-IO-Compress-L 100% | 215.2 MiB/s | 220.4 KiB | 00m00s [224/242] Installing perl-Archive-Tar-0 100% | 12.8 MiB/s | 156.9 KiB | 00m00s [225/242] Installing perl-File-Which-0: 100% | 0.0 B/s | 31.4 KiB | 00m00s [226/242] Installing perl-File-HomeDir- 100% | 120.9 MiB/s | 123.8 KiB | 00m00s [227/242] Installing perl-Text-Template 100% | 111.3 MiB/s | 114.0 KiB | 00m00s [228/242] Installing perl-MRO-Compat-0: 100% | 0.0 B/s | 44.9 KiB | 00m00s [229/242] Installing perl-Package-Gener 100% | 0.0 B/s | 31.5 KiB | 00m00s [230/242] Installing perl-Sub-Exporter- 100% | 197.2 MiB/s | 201.9 KiB | 00m00s [231/242] Installing perl-Data-Section- 100% | 43.0 MiB/s | 44.1 KiB | 00m00s [232/242] Installing perl-Software-Lice 100% | 167.0 MiB/s | 513.2 KiB | 00m00s [233/242] Installing perl-Module-Build- 100% | 46.3 MiB/s | 663.2 KiB | 00m00s [234/242] Installing systemtap-sdt-deve 100% | 180.9 MiB/s | 185.2 KiB | 00m00s [235/242] Installing perl-devel-4:5.42. 100% | 190.4 MiB/s | 3.8 MiB | 00m00s [236/242] Installing perl-ExtUtils-CBui 100% | 99.7 MiB/s | 102.1 KiB | 00m00s [237/242] Installing perl-ExtUtils-Embe 100% | 0.0 B/s | 16.1 KiB | 00m00s [238/242] Installing perl-ExtUtils-Mini 100% | 0.0 B/s | 8.8 KiB | 00m00s [239/242] Installing perl-CPAN-0:2.38-5 100% | 111.5 MiB/s | 1.9 MiB | 00m00s [240/242] Installing perl-4:5.42.0-520. 100% | 0.0 B/s | 124.0 B | 00m00s [241/242] Installing annobin-plugin-gcc 100% | 65.8 MiB/s | 1.0 MiB | 00m00s [242/242] Installing gcc-plugin-annobin 100% | 458.0 KiB/s | 58.6 KiB | 00m00s Warning: skipped OpenPGP checks for 240 packages from repository: http_kojipkgs_fedoraproject_org_repos_f44_build_latest_basearch Complete! Finish: build setup for hmmer-3.3.2-11.fc44.src.rpm Start: rpmbuild hmmer-3.3.2-11.fc44.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1753315200 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.7ynPqN Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.tMTb3w + umask 022 + cd /builddir/build/BUILD/hmmer-3.3.2-build + cd /builddir/build/BUILD/hmmer-3.3.2-build + rm -rf hmmer-3.3.2 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/hmmer-3.3.2.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd hmmer-3.3.2 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (hmmer-3.3.2-chris.patch):' Patch #0 (hmmer-3.3.2-chris.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .chris --fuzz=0 patching file easel/esl_regexp.h patching file src/hmmpgmd.h patching file src/hmmpgmd_shard.h + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.BH0WVF + umask 022 + cd /builddir/build/BUILD/hmmer-3.3.2-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-hardened-ld-errors -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 hmmer-3.3.2 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -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-hardened-ld-errors -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 + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure --- ./configure.backup 2020-11-26 21:19:58.000000000 +0000 +++ ./configure 2025-10-07 18:13:07.073795278 +0000 @@ -1898,7 +1898,7 @@ #ifdef __cplusplus extern "C" #endif -char $2 (); +__attribute__ ((used)) char $2 (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup '/lt_cv_sys_global_symbol_to_cdecl=/s#(".*"|'\''.*'\'')#"sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./easel/config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./easel/config.sub ++ basename ./easel/config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./easel/config.sub '/usr/lib/rpm/redhat/config.sub' -> './easel/config.sub' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./easel/config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./easel/config.guess ++ basename ./easel/config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./easel/config.guess '/usr/lib/rpm/redhat/config.guess' -> './easel/config.guess' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.sub + '[' -f /usr/lib/rpm/redhat/config.sub ']' + /usr/bin/rm -f ./config.sub ++ basename ./config.sub + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.sub ./config.sub '/usr/lib/rpm/redhat/config.sub' -> './config.sub' + for i in $(find $(dirname ./configure) -name config.guess -o -name config.sub) ++ basename ./config.guess + '[' -f /usr/lib/rpm/redhat/config.guess ']' + /usr/bin/rm -f ./config.guess ++ basename ./config.guess + /usr/bin/cp -fv /usr/lib/rpm/redhat/config.guess ./config.guess '/usr/lib/rpm/redhat/config.guess' -> './config.guess' + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors' ']' ++ find . -name ltmain.sh ++ grep -q runstatedir=DIR ./configure + ./configure --build=x86_64-redhat-linux --host=x86_64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/bin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info configure: WARNING: unrecognized options: --disable-dependency-tracking configure: Configuring HMMER3 for your system. checking build system type... x86_64-redhat-linux-gnu checking host system type... x86_64-redhat-linux-gnu checking whether to compile using MPI... no checking for x86_64-redhat-linux-gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gcc option to accept ISO C99... none needed checking for gcc option to accept ISO Standard C... (cached) none needed checking how to run the C preprocessor... gcc -E checking for a BSD-compatible install... /usr/bin/install -c checking for x86_64-redhat-linux-strip... no checking for strip... strip checking for x86_64-redhat-linux-ranlib... no checking for ranlib... ranlib checking for ar... /usr/bin/ar checking whether ln -s works... yes checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking whether gcc is Clang... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking whether gcc can compile our Altivec/VMX code... no checking whether gcc can compile our SSE code... yes configure: Activating Intel/AMD SSE vector DP implementation checking whether _MM_SET_FLUSH_ZERO_MODE is supported... yes checking compiler support --start-group... yes checking for gzip... /usr/bin/gzip checking for python3... yes checking for library containing clock_gettime... none required checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking endian.h usability... yes checking endian.h presence... yes checking for endian.h... yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking netinet/in.h usability... yes checking netinet/in.h presence... yes checking for netinet/in.h... yes checking sys/param.h usability... yes checking sys/param.h presence... yes checking for sys/param.h... yes checking for sys/sysctl.h... no checking for uint8_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for off_t... yes checking whether byte ordering is bigendian... no checking for __attribute__((noreturn))... yes checking for __attribute__((format))... yes checking for mkstemp... yes checking for popen... yes checking for putenv... yes checking for strcasecmp... yes checking for strsep... yes checking for times... yes checking for getpid... yes checking for sysctl... no checking for sysconf... yes checking for getcwd... yes checking for chmod... yes checking for stat... yes checking for fstat... yes checking for erfc... no checking for library containing ntohs... none required checking for library containing ntohl... none required checking for library containing htons... none required checking for library containing htonl... none required checking for library containing socket... none required checking for library containing inet_pton... none required checking for _LARGEFILE_SOURCE value needed for large files... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating testsuite/Makefile config.status: creating profmark/Makefile config.status: creating src/impl_sse/Makefile config.status: creating documentation/Makefile config.status: creating documentation/man/Makefile config.status: creating documentation/userguide/Makefile config.status: creating documentation/userguide/inclusions/Makefile config.status: creating libdivsufsort/Makefile config.status: creating easel/Makefile config.status: creating easel/miniapps/Makefile config.status: creating easel/testsuite/Makefile config.status: creating easel/documentation/Makefile config.status: creating documentation/userguide/titlepage.tex config.status: creating documentation/userguide/titlepage_daemon.tex config.status: creating documentation/userguide/copyright.tex config.status: creating documentation/man/alimask.man config.status: creating documentation/man/hmmalign.man config.status: creating documentation/man/hmmbuild.man config.status: creating documentation/man/hmmc2.man config.status: creating documentation/man/hmmconvert.man config.status: creating documentation/man/hmmemit.man config.status: creating documentation/man/hmmer.man config.status: creating documentation/man/hmmfetch.man config.status: creating documentation/man/hmmlogo.man config.status: creating documentation/man/hmmpgmd.man config.status: creating documentation/man/hmmpgmd_shard.man config.status: creating documentation/man/hmmpress.man config.status: creating documentation/man/hmmscan.man config.status: creating documentation/man/hmmsearch.man config.status: creating documentation/man/hmmsim.man config.status: creating documentation/man/hmmstat.man config.status: creating documentation/man/jackhmmer.man config.status: creating documentation/man/makehmmerdb.man config.status: creating documentation/man/nhmmer.man config.status: creating documentation/man/nhmmscan.man config.status: creating documentation/man/phmmer.man config.status: creating easel/miniapps/esl-afetch.man config.status: creating easel/miniapps/esl-alimanip.man config.status: creating easel/miniapps/esl-alimap.man config.status: creating easel/miniapps/esl-alimask.man config.status: creating easel/miniapps/esl-alimerge.man config.status: creating easel/miniapps/esl-alipid.man config.status: creating easel/miniapps/esl-alirev.man config.status: creating easel/miniapps/esl-alistat.man config.status: creating easel/miniapps/esl-compalign.man config.status: creating easel/miniapps/esl-compstruct.man config.status: creating easel/miniapps/esl-construct.man config.status: creating easel/miniapps/esl-histplot.man config.status: creating easel/miniapps/esl-mask.man config.status: creating easel/miniapps/esl-mixdchlet.man config.status: creating easel/miniapps/esl-reformat.man config.status: creating easel/miniapps/esl-selectn.man config.status: creating easel/miniapps/esl-seqrange.man config.status: creating easel/miniapps/esl-seqstat.man config.status: creating easel/miniapps/esl-sfetch.man config.status: creating easel/miniapps/esl-shuffle.man config.status: creating easel/miniapps/esl-ssdraw.man config.status: creating easel/miniapps/esl-translate.man config.status: creating easel/miniapps/esl-weight.man config.status: creating easel/decoy_config.h config.status: creating src/p7_config.h config.status: creating easel/esl_config.h config.status: creating libdivsufsort/divsufsort.h config.status: linking src/impl_sse to src/impl configure: WARNING: unrecognized options: --disable-dependency-tracking HMMER configuration: compiler: gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread host: x86_64-redhat-linux-gnu linker: -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-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes libraries: DP implementation: sse Now do 'make' to build HMMER, and optionally: 'make check' to run self tests, 'make install' to install programs and man pages, '(cd easel; make install)' to install Easel tools. + make -j4 SUBDIR easel CC easel.o CC esl_alloc.o CC esl_alphabet.o CC esl_arr2.o CC esl_arr3.o CC esl_bitfield.o CC esl_buffer.o CC esl_cluster.o CC esl_composition.o CC esl_cpu.o CC esl_dirichlet.o CC esl_distance.o CC esl_dmatrix.o CC esl_dsqdata.o CC esl_exponential.o CC esl_fileparser.o CC esl_gamma.o CC esl_gencode.o CC esl_getopts.o CC esl_gev.o CC esl_graph.o CC esl_gumbel.o CC esl_heap.o CC esl_histogram.o CC esl_hmm.o CC esl_huffman.o CC esl_hyperexp.o CC esl_json.o CC esl_keyhash.o CC esl_matrixops.o esl_json.c: In function ‘esl_json_Validate’: esl_json.c:752:33: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 752 | case eslJSON_BOOLEAN: if (! esl_memstrcmp(bf->mem + pos1, pos2-pos1+1, "true") && | ^~ esl_json.c:753:167: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 753 | ! esl_memstrcmp(bf->mem + pos1, pos2-pos1+1, "false")) ESL_FAIL(eslFAIL, errbuf, "boolean isn't a boolean, tok %d", i); break; | ^~~~~ CC esl_mem.o CC esl_minimizer.o CC esl_mixdchlet.o esl_minimizer.c: In function ‘esl_min_ConjugateGradientDescent’: esl_minimizer.c:243:23: warning: ‘fx’ may be used uninitialized [-Wmaybe-uninitialized] 243 | if (opt_fx) *opt_fx = fx; | ~~~~~~~~^~~~ esl_minimizer.c:119:10: note: ‘fx’ was declared here 119 | double fx; | ^~ In function ‘brent’, inlined from ‘esl_min_ConjugateGradientDescent’ at esl_minimizer.c:192:7: esl_minimizer.c:720:21: warning: ‘ax’ may be used uninitialized [-Wmaybe-uninitialized] 720 | m = 0.5 * (a+b); | ~~^~~ esl_minimizer.c: In function ‘esl_min_ConjugateGradientDescent’: esl_minimizer.c:118:10: note: ‘ax’ was declared here 118 | double ax,bx,cx; | ^~ In function ‘brent’, inlined from ‘esl_min_ConjugateGradientDescent’ at esl_minimizer.c:192:7: esl_minimizer.c:720:21: warning: ‘cx’ may be used uninitialized [-Wmaybe-uninitialized] 720 | m = 0.5 * (a+b); | ~~^~~ esl_minimizer.c: In function ‘esl_min_ConjugateGradientDescent’: esl_minimizer.c:118:16: note: ‘cx’ was declared here 118 | double ax,bx,cx; | ^~ CC esl_mixgev.o CC esl_mpi.o CC esl_msa.o CC esl_msacluster.o CC esl_msafile.o CC esl_msafile2.o CC esl_msafile_a2m.o CC esl_msafile_afa.o CC esl_msafile_clustal.o CC esl_msafile_phylip.o In function ‘phylip_interleaved_Read’, inlined from ‘esl_msafile_phylip_Read’ at esl_msafile_phylip.c:284:56: esl_msafile_phylip.c:452:15: warning: ‘block_alen’ may be used uninitialized [-Wmaybe-uninitialized] 452 | else if (cur_alen - alen != block_alen) ESL_XFAIL(eslEFORMAT, afp->errmsg, "number of residues on line differs from previous seqs in alignment block"); | ^ esl_msafile_phylip.c: In function ‘esl_msafile_phylip_Read’: esl_msafile_phylip.c:422:13: note: ‘block_alen’ was declared here 422 | int64_t block_alen; /* # of residues being added by current block */ | ^~~~~~~~~~ CC esl_msafile_psiblast.o CC esl_msafile_selex.o In function ‘phylip_check_interleaved’, inlined from ‘esl_msafile_phylip_CheckFileFormat’ at esl_msafile_phylip.c:389:13: esl_msafile_phylip.c:739:16: warning: ‘nres1’ may be used uninitialized [-Wmaybe-uninitialized] 739 | if (nres1+nres2 == alen) break; | ~~~~~^~~~~~ esl_msafile_phylip.c: In function ‘esl_msafile_phylip_CheckFileFormat’: esl_msafile_phylip.c:687:13: note: ‘nres1’ was declared here 687 | int nres1; | ^~~~~ In function ‘phylip_deduce_namewidth’, inlined from ‘phylip_check_interleaved’ at esl_msafile_phylip.c:747:22, inlined from ‘esl_msafile_phylip_CheckFileFormat’ at esl_msafile_phylip.c:389:13: esl_msafile_phylip.c:1048:10: warning: ‘ncols0’ may be used uninitialized [-Wmaybe-uninitialized] 1048 | for (c = ncols0-1; nres1 && c >= 0; c--) | ~~^~~~~~~~~~ esl_msafile_phylip.c: In function ‘esl_msafile_phylip_CheckFileFormat’: esl_msafile_phylip.c:683:20: note: ‘ncols0’ was declared here 683 | int ncols, ncols0; | ^~~~~~ CC esl_msafile_stockholm.o CC esl_msashuffle.o CC esl_msaweight.o CC esl_normal.o CC esl_paml.o CC esl_quicksort.o CC esl_random.o CC esl_rand64.o esl_msaweight.c: In function ‘esl_msaweight_IDFilter_adv’: esl_msaweight.c:1035:9: warning: ‘conscols_103’ may be used uninitialized [-Wmaybe-uninitialized] 1035 | collect_counts(cfg, msa, conscols, ncons, ct, NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ esl_msaweight.c:435:1: note: by argument 3 of type ‘const int *’ to ‘collect_counts.isra.0’ declared here 435 | collect_counts(const ESL_MSAWEIGHT_CFG *cfg, const ESL_MSA *msa, const int *conscols, int ncons, int **ct, ESL_MSAWEIGHT_DAT *dat) | ^~~~~~~~~~~~~~ CC esl_randomseq.o CC esl_ratematrix.o CC esl_recorder.o CC esl_red_black.o CC esl_regexp.o CC esl_rootfinder.o CC esl_scorematrix.o CC esl_sq.o CC esl_sqio.o In file included from esl_scorematrix.c:22: esl_scorematrix.c: In function ‘esl_scorematrix_Create’: easel.h:164:17: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 164 | if ( ((p) = malloc(size)) == NULL) { \ | ^~~~~~~~~~~~ In file included from easel.h:21: /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ In function ‘esl_sq_DestroyBlock’, inlined from ‘esl_sq_DestroyBlock’ at esl_sq.c:583:1, inlined from ‘sq_createblock’ at esl_sq.c:2152:3: esl_sq.c:589:24: warning: ‘block_15->listSize’ may be used uninitialized [-Wmaybe-uninitialized] 589 | for (i = 0; i < block->listSize; ++i) | ~~~~~^~~~~~~~~~ esl_sq.c:589:24: warning: ‘block_15->listSize’ may be used uninitialized [-Wmaybe-uninitialized] CC esl_sqio_ascii.o CC esl_sqio_ncbi.o CC esl_ssi.o CC esl_stack.o CC esl_stats.o CC esl_stopwatch.o CC esl_stretchexp.o CC esl_subcmd.o CC esl_threads.o CC esl_tree.o CC esl_varint.o CC esl_vectorops.o esl_varint.c: In function ‘esl_varint_google_decode’: esl_varint.c:474:11: warning: ‘grp’ may be used uninitialized [-Wmaybe-uninitialized] 474 | if (grp & cmask) { status = eslEOD; goto ERROR; } | ~~~~^~~~~~~ esl_varint.c:464:12: note: ‘grp’ was declared here 464 | uint64_t grp; // current k-bit code group | ^~~ CC esl_weibull.o CC esl_workqueue.o CC esl_wuss.o CC esl_sse.o esl_wuss.c: In function ‘esl_wuss2ct’: esl_wuss.c:136:10: warning: ‘status’ may be used uninitialized [-Wmaybe-uninitialized] 136 | return status; | ^~~~~~ esl_wuss.c:56:14: note: ‘status’ was declared here 56 | int status; /* success or failure return status */ | ^~~~~~ CC esl_avx.o CC esl_avx512.o CC esl_neon.o CC esl_vmx.o AR libeasel.a SUBDIR miniapps GEN esl-afetch GEN esl-alimap GEN esl-alimanip GEN esl-alimask esl-alimask.c: In function ‘main’: esl-alimask.c:1007:7: warning: ‘ppidx_thresh’ may be used uninitialized [-Wmaybe-uninitialized] 1007 | int ppidx_thresh; | ^~~~~~~~~~~~ GEN esl-alimerge esl-alimerge.c: In function ‘validate_and_copy_msa_annotation’: esl-alimerge.c:732:7: warning: ‘found_tag’ may be used uninitialized [-Wmaybe-uninitialized] 732 | int found_tag; | ^~~~~~~~~ In file included from /usr/include/stdio.h:970, from esl-alimerge.c:26: In function ‘fprintf’, inlined from ‘main’ at esl-alimerge.c:366:2: /usr/include/bits/stdio2.h:111:10: warning: ‘namewidth’ may be used uninitialized [-Wmaybe-uninitialized] 111 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ esl-alimerge.c: In function ‘main’: esl-alimerge.c:136:14: note: ‘namewidth’ was declared here 136 | int namewidth; /* max width of file name */ | ^~~~~~~~~ esl-alimerge.c:412:16: warning: ‘clen’ may be used uninitialized [-Wmaybe-uninitialized] 412 | if((status = validate_and_copy_msa_annotation(go, outfmt, mmsa, msaA, nali_tot, clen, alen_mmsa, maxgap, maxmis, errbuf)) != eslOK) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ esl-alimerge.c:118:17: note: ‘clen’ was declared here 118 | int clen; /* consensus length (non-gap #=GC RF length) of all alignments */ | ^~~~ GEN esl-alipid GEN esl-alirev GEN esl-alistat GEN esl-compalign In file included from /usr/include/stdio.h:970, from esl-alistat.c:6: In function ‘printf’, inlined from ‘main’ at esl-alistat.c:293:6: /usr/include/bits/stdio2.h:118:10: warning: ‘small’ may be used uninitialized [-Wmaybe-uninitialized] 118 | return __printf_chk (__USE_FORTIFY_LEVEL - 1, __fmt, __va_arg_pack ()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ esl-alistat.c: In function ‘main’: esl-alistat.c:74:17: note: ‘small’ was declared here 74 | int64_t small, large; /* smallest, largest sequence */ | ^~~~~ In function ‘printf’, inlined from ‘main’ at esl-alistat.c:294:6: /usr/include/bits/stdio2.h:118:10: warning: ‘large’ may be used uninitialized [-Wmaybe-uninitialized] 118 | return __printf_chk (__USE_FORTIFY_LEVEL - 1, __fmt, __va_arg_pack ()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ esl-alistat.c: In function ‘main’: esl-alistat.c:74:24: note: ‘large’ was declared here 74 | int64_t small, large; /* smallest, largest sequence */ | ^~~~~ esl-compalign.c: In function ‘main’: esl-compalign.c:231:13: warning: ‘masklen’ may be used uninitialized [-Wmaybe-uninitialized] 231 | if(masklen != rflen) { | ^ esl-compalign.c:90:7: note: ‘masklen’ was declared here 90 | int masklen; | ^~~~~~~ esl-compalign.c:322:45: warning: ‘ppidx’ may be used uninitialized [-Wmaybe-uninitialized] 322 | if(do_post_for_this_rfpos) ptm[ppidx]++; | ^ esl-compalign.c:104:7: note: ‘ppidx’ was declared here 104 | int ppidx; /* index of PP */ | ^~~~~ GEN esl-compstruct GEN esl-construct GEN esl-histplot esl-construct.c: In function ‘main’: esl-construct.c:573:24: warning: ‘fmin’ may be used uninitialized [-Wmaybe-uninitialized] 573 | if(do_fmin) { printf("#\n# determined to be %.3f\n", fthresh); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ esl-construct.c:129:9: note: ‘fmin’ was declared here 129 | float fmin; | ^~~~ GEN esl-mask GEN esl-mixdchlet GEN esl-reformat GEN esl-selectn esl-reformat.c: In function ‘main’: esl-reformat.c:416:9: warning: ‘mapfp’ may be used uninitialized [-Wmaybe-uninitialized] 416 | fclose(mapfp); | ^~~~~~~~~~~~~ esl-reformat.c:304:20: note: ‘mapfp’ was declared here 304 | FILE *mapfp; /* output stream for the map file */ | ^~~~~ esl-reformat.c:212:13: warning: ‘reached_eof’ may be used uninitialized [-Wmaybe-uninitialized] 212 | if(! reached_eof) esl_fatal("Input file contains >1 alignments, but afa formatted output file can only contain 1"); | ^ esl-reformat.c:103:10: note: ‘reached_eof’ was declared here 103 | int reached_eof; /* reached EOF? used only in small mem mode */ | ^~~~~~~~~~~ GEN esl-seqrange GEN esl-seqstat GEN esl-sfetch GEN esl-shuffle GEN esl-ssdraw esl-ssdraw.c: In function ‘get_insert_info_from_ifile.constprop.0’: esl-ssdraw.c:6664:32: warning: ‘rfpos’ may be used uninitialized [-Wmaybe-uninitialized] 6664 | if(! seen_end_of_model_line) esl_fatal("Error reading insert file, didn't read the special '//' line at the end of file %s.\n", rfpos, efp->linenumber, ifile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ esl-ssdraw.c:6500:19: note: ‘rfpos’ was declared here 6500 | int rfpos; /* current nongap RF position */ | ^~~~~ In file included from esl-ssdraw.c:16: In function ‘draw_header_and_footer’, inlined from ‘draw_sspostscript.isra.0’ at esl-ssdraw.c:2491:18: esl-ssdraw.c:6263:56: warning: ‘split_idx’ may be used uninitialized [-Wmaybe-uninitialized] 6263 | ESL_ALLOC(desc2print, sizeof(char) * (split_idx+1)); | ~~~~~~~~~~^~~ esl-ssdraw.c: In function ‘draw_sspostscript.isra.0’: esl-ssdraw.c:6164:10: note: ‘split_idx’ was declared here 6164 | int i, split_idx; | ^~~~~~~~~ In file included from /usr/include/stdio.h:970, from esl-ssdraw.c:10: In function ‘fprintf’, inlined from ‘individuals_sspostscript.constprop.0’ at esl-ssdraw.c:3663:7: /usr/include/bits/stdio2.h:111:10: warning: ‘namewidth’ may be used uninitialized [-Wmaybe-uninitialized] 111 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ esl-ssdraw.c: In function ‘individuals_sspostscript.constprop.0’: esl-ssdraw.c:3347:7: note: ‘namewidth’ was declared here 3347 | int namewidth; /* length in chars of longest seq name we'll print */ | ^~~~~~~~~ GEN esl-translate esl-ssdraw.c: In function ‘parse_template_file.isra.0’: esl-ssdraw.c:2716:10: warning: ‘ps’ may be used uninitialized [-Wmaybe-uninitialized] 2716 | if(ps->rflen == msa_rflen) { found_match = TRUE; } | ~~^~~~~~~ esl-ssdraw.c:2703:19: note: ‘ps’ was declared here 2703 | SSPostscript_t *ps; | ^~ GEN esl-weight CC cmd_alistat.o CC cmd_downsample.o CC cmd_filter.o CC cmd_index.o GEN easel SUBDIR libdivsufsort CC divsufsort.o AR libdivsufsort.a SUBDIR src CC alimask.o CC build.o CC cachedb.o CC cachedb_shard.o alimask.c: In function ‘main’: alimask.c:313:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 313 | if (puts("Must specify mask range with --modelrange, --alirange, --model2ali, or --ali2model\n") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto ERROR; | ^~ alimask.c:313:154: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 313 | if (puts("Must specify mask range with --modelrange, --alirange, --model2ali, or --ali2model\n") < 0) ESL_XEXCEPTION_SYS(eslEWRITE, "write failed"); goto ERROR; | ^~~~ CC emit.o CC errors.o CC evalues.o CC eweight.o CC generic_decoding.o CC generic_fwdback.o CC generic_fwdback_chk.o CC generic_fwdback_banded.o CC generic_null2.o CC generic_msv.o CC generic_optacc.o CC generic_stotrace.o CC generic_viterbi.o CC generic_vtrace.o generic_stotrace.c: In function ‘p7_GStochasticTrace’: generic_stotrace.c:172:21: warning: ‘scur’ may be used uninitialized [-Wmaybe-uninitialized] 172 | if ((status = p7_trace_Append(tr, scur, k, i)) != eslOK) goto ERROR; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ generic_stotrace.c:57:11: note: ‘scur’ was declared here 57 | int scur, sprv; | ^~~~ CC h2_io.o CC heatmap.o CC hmmlogo.o CC hmmdmstr.o CC hmmdmstr_shard.o CC hmmd_search_status.o CC hmmdwrkr.o CC hmmdwrkr_shard.o In function ‘process_ServerCmd’, inlined from ‘clientside_loop’ at hmmdmstr.c:1134:5: hmmdmstr.c:1020:24: warning: array subscript ‘struct HMMD_COMMAND[0]’ is partly outside array bounds of ‘unsigned char[12]’ [-Warray-bounds=] 1020 | cmd->hdr.command = HMMD_CMD_SHUTDOWN; hmmdmstr.c:1017:18: note: object of size 12 allocated by ‘malloc’ 1017 | if ((cmd = malloc(sizeof(HMMD_HEADER))) == NULL) LOG_FATAL_MSG("malloc", errno); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmdmstr.c:1046:3: warning: array subscript ‘struct HMMD_COMMAND[0]’ is partly outside array bounds of ‘unsigned char[12]’ [-Warray-bounds=] 1046 | printf("Queuing command %d from %s (%d)\n", cmd->hdr.command, parms->ip_addr, parms->sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmdmstr.c:1017:18: note: object of size 12 allocated by ‘malloc’ 1017 | if ((cmd = malloc(sizeof(HMMD_HEADER))) == NULL) LOG_FATAL_MSG("malloc", errno); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘process_ServerCmd’, inlined from ‘clientside_loop’ at hmmdmstr_shard.c:1173:5: hmmdmstr_shard.c:1059:24: warning: array subscript ‘struct HMMD_COMMAND_SHARD[0]’ is partly outside array bounds of ‘unsigned char[12]’ [-Warray-bounds=] 1059 | cmd->hdr.command = HMMD_CMD_SHUTDOWN; hmmdmstr_shard.c:1056:18: note: object of size 12 allocated by ‘malloc’ 1056 | if ((cmd = malloc(sizeof(HMMD_HEADER))) == NULL) LOG_FATAL_MSG("malloc", errno); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmdmstr_shard.c:1085:3: warning: array subscript ‘struct HMMD_COMMAND_SHARD[0]’ is partly outside array bounds of ‘unsigned char[12]’ [-Warray-bounds=] 1085 | printf("Queuing command %d from %s (%d)\n", cmd->hdr.command, parms->ip_addr, parms->sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmdmstr_shard.c:1056:18: note: object of size 12 allocated by ‘malloc’ 1056 | if ((cmd = malloc(sizeof(HMMD_HEADER))) == NULL) LOG_FATAL_MSG("malloc", errno); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ CC hmmdutils.o CC hmmer.o CC logsum.o CC modelconfig.o CC modelstats.o CC mpisupport.o CC seqmodel.o CC tracealign.o CC p7_bg.o CC p7_alidisplay.o CC p7_builder.o CC p7_domain.o p7_domain.c: In function ‘p7_domain_Serialize’: p7_domain.c:191:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 191 | network_32bit = esl_hton32(*((uint32_t *) &(obj->envsc))); // ow, this hurts, but is probably the best way to get the | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ p7_domain.c:198:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 198 | network_32bit = esl_hton32(*((uint32_t *) &(obj->domcorrection))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ p7_domain.c:203:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | network_32bit = esl_hton32(*((uint32_t *) &(obj->dombias))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ p7_domain.c:208:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 208 | network_32bit = esl_hton32(*((uint32_t *) &(obj->oasc))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~ p7_domain.c:213:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 213 | network_32bit = esl_hton32(*((uint32_t *) &(obj->bitscore))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ p7_domain.c:218:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 218 | network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~ p7_domain.c: In function ‘p7_domain_Deserialize’: p7_domain.c:341:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 341 | ret_obj->envsc = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ p7_domain.c:347:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | ret_obj->domcorrection = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ p7_domain.c:353:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 353 | ret_obj->dombias = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ p7_domain.c:359:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 359 | ret_obj->oasc = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ p7_domain.c:365:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 365 | ret_obj->bitscore = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ p7_domain.c:371:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 371 | ret_obj->lnP = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ p7_domain.c:398:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 398 | ret_obj->scores_per_pos[i] = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ CC p7_domaindef.o CC p7_gbands.o CC p7_gmx.o p7_domaindef.c: In function ‘rescore_isolated_domain’: p7_domaindef.c:932:5: warning: ‘orig_L’ may be used uninitialized [-Wmaybe-uninitialized] 932 | p7_oprofile_ReconfigRestLength(om, orig_L); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ p7_domaindef.c:827:18: note: ‘orig_L’ was declared here 827 | int orig_L; | ^~~~~~ CC p7_gmxb.o CC p7_gmxchk.o CC p7_hit.o CC p7_hmm.o CC p7_hmmcache.o p7_hit.c: In function ‘p7_hit_Serialize’: p7_hit.c:226:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 226 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sortkey))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:231:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 231 | network_32bit = esl_hton32(*((uint32_t *) &(obj->score))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:236:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 236 | network_32bit = esl_hton32(*((uint32_t *) &(obj->pre_score))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:241:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 241 | network_32bit = esl_hton32(*((uint32_t *) &(obj->sum_score))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:246:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 246 | network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:251:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 251 | network_64bit = esl_hton64(*((uint64_t *) &(obj->pre_lnP))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:256:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 256 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sum_lnP))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:261:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 261 | network_32bit = esl_hton32(*((uint32_t *) &(obj->nexpected))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ p7_hit.c: In function ‘p7_hit_Deserialize’: p7_hit.c:408:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 408 | ret_obj->sortkey = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:414:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 414 | ret_obj->score = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:420:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 420 | ret_obj->pre_score = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:426:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 426 | ret_obj->sum_score = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:432:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 432 | ret_obj->lnP = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:438:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 438 | ret_obj->pre_lnP = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:444:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 444 | ret_obj->sum_lnP = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ p7_hit.c:450:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 450 | ret_obj->nexpected = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ CC p7_hmmd_search_stats.o p7_hmmd_search_stats.c: In function ‘p7_hmmd_search_stats_Serialize’: p7_hmmd_search_stats.c:89:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 89 | network_64bit = esl_hton64(*((uint64_t *) &(obj->elapsed))); // ow, this hurts, but is probably the best way to get the | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ p7_hmmd_search_stats.c:97:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 97 | network_64bit = esl_hton64(*((uint64_t *) &(obj->user))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~ p7_hmmd_search_stats.c:103:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 103 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sys))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~ p7_hmmd_search_stats.c:109:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 109 | network_64bit = esl_hton64(*((uint64_t *) &(obj->Z))); | ~^~~~~~~~~~~~~~~~~~~~~~~ p7_hmmd_search_stats.c:115:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 115 | network_64bit = esl_hton64(*((uint64_t *) &(obj->domZ))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~ p7_hmmd_search_stats.c: In function ‘p7_hmmd_search_stats_Deserialize’: p7_hmmd_search_stats.c:256:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 256 | ret_obj->elapsed = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ p7_hmmd_search_stats.c:262:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 262 | ret_obj->user = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ p7_hmmd_search_stats.c:268:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 268 | ret_obj->sys = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ p7_hmmd_search_stats.c:274:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 274 | ret_obj->Z = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ p7_hmmd_search_stats.c:280:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 280 | ret_obj->domZ = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ CC p7_hmmfile.o CC p7_hmmwindow.o CC p7_pipeline.o CC p7_prior.o CC p7_profile.o CC p7_spensemble.o In file included from p7_spensemble.c:7: p7_spensemble.c: In function ‘p7_spensemble_Cluster’: p7_spensemble.c:344:43: warning: ‘imax’ may be used uninitialized [-Wmaybe-uninitialized] 344 | cwindow_width = ESL_MAX(ESL_MAX(imax-imin+1, jmax-jmin+1), | ~~~~^~~~~ p7_spensemble.c:294:7: note: ‘imax’ was declared here 294 | int imax, jmax, kmax, mmax; | ^~~~ p7_spensemble.c:344:56: warning: ‘jmin’ may be used uninitialized [-Wmaybe-uninitialized] 344 | cwindow_width = ESL_MAX(ESL_MAX(imax-imin+1, jmax-jmin+1), | ~~~~^~~~~ p7_spensemble.c:293:13: note: ‘jmin’ was declared here 293 | int imin, jmin, kmin, mmin; | ^~~~ p7_spensemble.c:345:43: warning: ‘kmin’ may be used uninitialized [-Wmaybe-uninitialized] 345 | ESL_MAX(kmax-kmin+1, mmax-mmin+1)); | ~~~~^~~~~ p7_spensemble.c:293:19: note: ‘kmin’ was declared here 293 | int imin, jmin, kmin, mmin; | ^~~~ p7_spensemble.c:345:56: warning: ‘mmin’ may be used uninitialized [-Wmaybe-uninitialized] 345 | ESL_MAX(kmax-kmin+1, mmax-mmin+1)); | ~~~~^~~~~ p7_spensemble.c:293:25: note: ‘mmin’ was declared here 293 | int imin, jmin, kmin, mmin; | ^~~~ p7_spensemble.c:344:56: warning: ‘jmax’ may be used uninitialized [-Wmaybe-uninitialized] 344 | cwindow_width = ESL_MAX(ESL_MAX(imax-imin+1, jmax-jmin+1), | ~~~~^~~~~ p7_spensemble.c:294:13: note: ‘jmax’ was declared here 294 | int imax, jmax, kmax, mmax; | ^~~~ p7_spensemble.c:345:43: warning: ‘kmax’ may be used uninitialized [-Wmaybe-uninitialized] 345 | ESL_MAX(kmax-kmin+1, mmax-mmin+1)); | ~~~~^~~~~ p7_spensemble.c:294:19: note: ‘kmax’ was declared here 294 | int imax, jmax, kmax, mmax; | ^~~~ p7_spensemble.c:345:56: warning: ‘mmax’ may be used uninitialized [-Wmaybe-uninitialized] 345 | ESL_MAX(kmax-kmin+1, mmax-mmin+1)); | ~~~~^~~~~ p7_spensemble.c:294:25: note: ‘mmax’ was declared here 294 | int imax, jmax, kmax, mmax; | ^~~~ CC p7_tophits.o CC p7_trace.o CC p7_scoredata.o CC hmmpgmd2msa.o In file included from /usr/include/stdio.h:970, from ../easel/easel.h:22, from p7_tophits.c:16: In function ‘fprintf’, inlined from ‘p7_tophits_Targets’ at p7_tophits.c:1142:12: /usr/include/bits/stdio2.h:111:10: warning: ‘posw’ may be used uninitialized [-Wmaybe-uninitialized] 111 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ p7_tophits.c: In function ‘p7_tophits_Targets’: p7_tophits.c:1068:10: note: ‘posw’ was declared here 1068 | int posw; | ^~~~ CC fm_alphabet.o CC fm_general.o CC fm_sse.o CC fm_ssv.o CC hmmalign.o In function ‘FM_extendSeed’, inlined from ‘p7_SSVFM_longlarget’ at fm_ssv.c:806:5: fm_ssv.c:696:32: warning: ‘max_hit_start’ may be used uninitialized [-Wmaybe-uninitialized] 696 | diag->k = model_start + max_hit_start - 1; | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~ fm_ssv.c: In function ‘p7_SSVFM_longlarget’: fm_ssv.c:648:22: note: ‘max_hit_start’ was declared here 648 | int64_t hit_start, max_hit_start, max_hit_end; | ^~~~~~~~~~~~~ In function ‘FM_extendSeed’, inlined from ‘p7_SSVFM_longlarget’ at fm_ssv.c:806:5: fm_ssv.c:697:31: warning: ‘max_hit_end’ may be used uninitialized [-Wmaybe-uninitialized] 697 | diag->length = max_hit_end - max_hit_start + 1; | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ fm_ssv.c: In function ‘p7_SSVFM_longlarget’: fm_ssv.c:648:37: note: ‘max_hit_end’ was declared here 648 | int64_t hit_start, max_hit_start, max_hit_end; | ^~~~~~~~~~~ CC hmmbuild.o CC hmmconvert.o CC hmmemit.o CC hmmfetch.o CC hmmpgmd.o CC hmmpgmd_shard.o CC hmmpress.o CC hmmscan.o CC hmmsearch.o CC hmmsim.o CC hmmstat.o CC jackhmmer.o In function ‘output_filter_power’, inlined from ‘output_result’ at hmmsim.c:756:38, inlined from ‘serial_master’ at hmmsim.c:384:11, inlined from ‘main’ at hmmsim.c:248:7: hmmsim.c:902:25: warning: ‘mu’ may be used uninitialized [-Wmaybe-uninitialized] 902 | esl_exp_surv (scores[i], pmu, plambda)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmsim.c: In function ‘main’: hmmsim.c:360:15: note: ‘mu’ was declared here 360 | double mu, lambda; | ^~ In function ‘output_filter_power’, inlined from ‘output_result’ at hmmsim.c:756:38, inlined from ‘serial_master’ at hmmsim.c:384:11, inlined from ‘main’ at hmmsim.c:248:7: hmmsim.c:902:25: warning: ‘lambda’ may be used uninitialized [-Wmaybe-uninitialized] 902 | esl_exp_surv (scores[i], pmu, plambda)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hmmsim.c: In function ‘main’: hmmsim.c:360:19: note: ‘lambda’ was declared here 360 | double mu, lambda; | ^~~~~~ CC phmmer.o CC nhmmer.o CC nhmmscan.o CC makehmmerdb.o CC hmmc2.o In function ‘serial_loop’, inlined from ‘serial_master’ at nhmmer.c:1071:35: nhmmer.c:1367:41: warning: ‘dbsq_revcmp’ may be used uninitialized [-Wmaybe-uninitialized] 1367 | info->pli->nres += dbsq_revcmp->W; | ~~~~~~~~~~~^~~ nhmmer.c: In function ‘serial_master’: nhmmer.c:1338:13: note: ‘dbsq_revcmp’ was declared here 1338 | ESL_SQ *dbsq_revcmp; | ^~~~~~~~~~~ CC hmmerfm-exactmatch.o AR libhmmer-src.stamp SUBDIR impl_sse CC decoding.o In file included from /usr/include/stdio.h:970, from ../easel/easel.h:22, from hmmerfm-exactmatch.c:6: In function ‘fprintf’, inlined from ‘output_header’ at hmmerfm-exactmatch.c:123:7, inlined from ‘main’ at hmmerfm-exactmatch.c:303:3: /usr/include/bits/stdio2.h:111:10: warning: ‘alph’ may be used uninitialized [-Wmaybe-uninitialized] 111 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ hmmerfm-exactmatch.c: In function ‘main’: hmmerfm-exactmatch.c:94:9: note: ‘alph’ was declared here 94 | char *alph; | ^~~~ CC fwdback.o CC io.o CC ssvfilter.o CC msvfilter.o CC null2.o CC optacc.o CC stotrace.o CC vitfilter.o In function ‘get_postprob’, inlined from ‘p7_OATrace’ at optacc.c:254:18: optacc.c:273:3: warning: ‘smax’ may be used uninitialized [-Wmaybe-uninitialized] 273 | switch (scur) { | ^~~~~~ optacc.c: In function ‘p7_OATrace’: optacc.c:398:10: note: ‘smax’ was declared here 398 | int smax, kmax; | ^~~~ In function ‘get_postprob’, inlined from ‘p7_OATrace’ at optacc.c:254:18: optacc.c:269:21: warning: ‘kmax’ may be used uninitialized [-Wmaybe-uninitialized] 269 | int q = (k-1) % Q; /* (q,r) is position of the current DP cell M(i,k) */ | ~~^~~ optacc.c: In function ‘p7_OATrace’: optacc.c:398:16: note: ‘kmax’ was declared here 398 | int smax, kmax; | ^~~~ CC p7_omx.o CC p7_oprofile.o CC mpi.o AR libhmmer-impl.stamp GEN alimask GEN hmmalign GEN hmmbuild GEN hmmconvert ../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ GEN hmmemit GEN hmmfetch GEN hmmlogo GEN hmmpgmd GEN hmmpgmd_shard ../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ GEN hmmpress ../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ GEN hmmscan GEN hmmsearch GEN hmmsim GEN hmmstat GEN jackhmmer GEN phmmer GEN nhmmer GEN nhmmscan ../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ ../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ ../easel/esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ../easel/esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ GEN makehmmerdb GEN hmmc2 GEN hmmerfm-exactmatch SUBDIR profmark CC create-profmark.o CC rocplot.o In file included from /usr/include/stdio.h:970, from create-profmark.c:18: In function ‘fprintf’, inlined from ‘main’ at create-profmark.c:258:4: /usr/include/bits/stdio2.h:111:10: warning: ‘nfrags’ may be used uninitialized [-Wmaybe-uninitialized] 111 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ create-profmark.c: In function ‘main’: create-profmark.c:167:17: note: ‘nfrags’ was declared here 167 | int nfrags; /* # of fragments removed */ | ^~~~~~ In function ‘synthesize_positives’, inlined from ‘main’ at create-profmark.c:253:4: create-profmark.c:536:27: warning: ‘j’ may be used uninitialized [-Wmaybe-uninitialized] 536 | memcpy(sq->dsq+j+d1n+1, domain2->dsq+1, sizeof(ESL_DSQ) * d2n); | ^ create-profmark.c: In function ‘main’: create-profmark.c:445:13: note: ‘j’ was declared here 445 | int i,j; | ^ GEN rocplot GEN create-profmark + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.M2sgkH + umask 022 + cd /builddir/build/BUILD/hmmer-3.3.2-build + '[' /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT ++ dirname /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT + mkdir -p /builddir/build/BUILD/hmmer-3.3.2-build + mkdir /builddir/build/BUILD/hmmer-3.3.2-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-hardened-ld-errors -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 hmmer-3.3.2 + rm -rf /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT + make install DESTDIR=/builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT SUBDIR easel SUBDIR miniapps SUBDIR libdivsufsort SUBDIR src SUBDIR impl_sse SUBDIR profmark /usr/bin/install -c -d /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/bin /usr/bin/install -c -d /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/man/man1 make -C src install make[1]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/src' for file in alimask hmmalign hmmbuild hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpgmd_shard hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer phmmer nhmmer nhmmscan makehmmerdb; do \ /usr/bin/install -c -m 0755 $file /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/bin/ ;\ done make[1]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/src' make -C documentation install make[1]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/documentation' make -C man install make[2]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/documentation/man' for file in hmmer hmmalign hmmbuild hmmc2 hmmconvert hmmemit hmmfetch hmmlogo hmmpgmd hmmpgmd_shard hmmpress hmmscan hmmsearch hmmsim hmmstat jackhmmer makehmmerdb phmmer nhmmer nhmmscan alimask; do \ /usr/bin/install -c -m 0664 $file.man /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/man/man1/${file}.1 ;\ done make[2]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/documentation/man' make[1]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/documentation' + cd easel + make install DESTDIR=/builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT /usr/bin/install -c -d /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/bin /usr/bin/install -c -d /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/man/man1 make -C miniapps install make[1]: Entering directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/easel/miniapps' /usr/bin/install -c -m 0755 easel /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/bin/ for file in esl-afetch esl-alimanip esl-alimap esl-alimask esl-alimerge esl-alipid esl-alirev esl-alistat esl-compalign esl-compstruct esl-construct esl-histplot esl-mask esl-mixdchlet esl-reformat esl-selectn esl-seqrange esl-seqstat esl-sfetch esl-shuffle esl-ssdraw esl-translate esl-weight; do \ /usr/bin/install -c -m 0755 $file /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/bin/ ;\ done for file in esl-afetch esl-alimanip esl-alimap esl-alimask esl-alimerge esl-alipid esl-alirev esl-alistat esl-compalign esl-compstruct esl-construct esl-histplot esl-mask esl-mixdchlet esl-reformat esl-selectn esl-seqrange esl-seqstat esl-sfetch esl-shuffle esl-ssdraw esl-translate esl-weight; do \ /usr/bin/install -c -m 0644 $file.man /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/man/man1/${file}.1 ;\ done make[1]: Leaving directory '/builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/easel/miniapps' + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 3.3.2-11.fc44 --unique-debug-suffix -3.3.2-11.fc44.x86_64 --unique-debug-src-base hmmer-3.3.2-11.fc44.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2 find-debuginfo: starting Extracting debug info from 43 files DWARF-compressing 43 files sepdebugcrcfix: Updated 43 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/hmmer-3.3.2-11.fc44.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/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-det --brp -j4 /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT Scanned 19 directories and 371 files, processed 44 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors + /usr/bin/linkdupes --brp /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr Scanned 18 directories and 371 files, considered 371 files, read 6 files, linked 0 files, 0 errors sum of sizes of linked files: 0 bytes Reading /builddir/build/BUILD/hmmer-3.3.2-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.4IsogE + umask 022 + cd /builddir/build/BUILD/hmmer-3.3.2-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-hardened-ld-errors -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 hmmer-3.3.2 + make check SUBDIR easel GEN easel_utest GEN esl_alloc_utest GEN esl_alphabet_utest GEN esl_bitfield_utest GEN esl_buffer_utest GEN esl_cluster_utest GEN esl_cpu_utest GEN esl_dirichlet_utest GEN esl_distance_utest GEN esl_dmatrix_utest GEN esl_dsqdata_utest GEN esl_exponential_utest GEN esl_fileparser_utest GEN esl_gamma_utest GEN esl_gencode_utest GEN esl_getopts_utest GEN esl_graph_utest GEN esl_gumbel_utest GEN esl_heap_utest GEN esl_histogram_utest GEN esl_hmm_utest GEN esl_huffman_utest GEN esl_hyperexp_utest GEN esl_json_utest ./esl_json.c: In function ‘esl_json_Validate’: ./esl_json.c:752:33: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 752 | case eslJSON_BOOLEAN: if (! esl_memstrcmp(bf->mem + pos1, pos2-pos1+1, "true") && | ^~ ./esl_json.c:753:167: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 753 | ! esl_memstrcmp(bf->mem + pos1, pos2-pos1+1, "false")) ESL_FAIL(eslFAIL, errbuf, "boolean isn't a boolean, tok %d", i); break; | ^~~~~ GEN esl_keyhash_utest In function ‘utest_stringkeys’, inlined from ‘main’ at ./esl_keyhash.c:875:3: ./esl_keyhash.c:786:54: warning: ‘h42’ may be used uninitialized [-Wmaybe-uninitialized] 786 | if ( esl_keyhash_Lookup(kh, "XX", -1, &h) != eslOK || h != h42) esl_fatal(msg); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ ./esl_keyhash.c: In function ‘main’: ./esl_keyhash.c:749:25: note: ‘h42’ was declared here 749 | int i,j,h,h42; | ^~~ In function ‘utest_memkeys’, inlined from ‘main’ at ./esl_keyhash.c:876:3: ./esl_keyhash.c:835:62: warning: ‘h42’ may be used uninitialized [-Wmaybe-uninitialized] 835 | if ( esl_keyhash_Lookup(kh, keys[42], keylen, &h) != eslOK || h != h42) esl_fatal(msg); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ ./esl_keyhash.c: In function ‘main’: ./esl_keyhash.c:812:23: note: ‘h42’ was declared here 812 | int i,h,h42; | ^~~ GEN esl_matrixops_utest GEN esl_mem_utest GEN esl_minimizer_utest ./esl_minimizer.c: In function ‘esl_min_ConjugateGradientDescent’: ./esl_minimizer.c:243:23: warning: ‘fx’ may be used uninitialized [-Wmaybe-uninitialized] 243 | if (opt_fx) *opt_fx = fx; | ~~~~~~~~^~~~ ./esl_minimizer.c:119:10: note: ‘fx’ was declared here 119 | double fx; | ^~ In function ‘brent’, inlined from ‘esl_min_ConjugateGradientDescent’ at ./esl_minimizer.c:192:7: ./esl_minimizer.c:720:21: warning: ‘ax’ may be used uninitialized [-Wmaybe-uninitialized] 720 | m = 0.5 * (a+b); | ~~^~~ ./esl_minimizer.c: In function ‘esl_min_ConjugateGradientDescent’: ./esl_minimizer.c:118:10: note: ‘ax’ was declared here 118 | double ax,bx,cx; | ^~ In function ‘brent’, inlined from ‘esl_min_ConjugateGradientDescent’ at ./esl_minimizer.c:192:7: ./esl_minimizer.c:720:21: warning: ‘cx’ may be used uninitialized [-Wmaybe-uninitialized] 720 | m = 0.5 * (a+b); | ~~^~~ ./esl_minimizer.c: In function ‘esl_min_ConjugateGradientDescent’: ./esl_minimizer.c:118:16: note: ‘cx’ was declared here 118 | double ax,bx,cx; | ^~ GEN esl_mixdchlet_utest GEN esl_msa_utest GEN esl_msacluster_utest GEN esl_msafile_utest GEN esl_msafile2_utest GEN esl_msafile_a2m_utest GEN esl_msafile_afa_utest GEN esl_msafile_clustal_utest GEN esl_msafile_phylip_utest In function ‘phylip_interleaved_Read’, inlined from ‘esl_msafile_phylip_Read’ at ./esl_msafile_phylip.c:284:56: ./esl_msafile_phylip.c:452:15: warning: ‘block_alen’ may be used uninitialized [-Wmaybe-uninitialized] 452 | else if (cur_alen - alen != block_alen) ESL_XFAIL(eslEFORMAT, afp->errmsg, "number of residues on line differs from previous seqs in alignment block"); | ^ ./esl_msafile_phylip.c: In function ‘esl_msafile_phylip_Read’: ./esl_msafile_phylip.c:422:13: note: ‘block_alen’ was declared here 422 | int64_t block_alen; /* # of residues being added by current block */ | ^~~~~~~~~~ In function ‘phylip_check_interleaved’, inlined from ‘esl_msafile_phylip_CheckFileFormat’ at ./esl_msafile_phylip.c:389:13: ./esl_msafile_phylip.c:739:16: warning: ‘nres1’ may be used uninitialized [-Wmaybe-uninitialized] 739 | if (nres1+nres2 == alen) break; | ~~~~~^~~~~~ ./esl_msafile_phylip.c: In function ‘esl_msafile_phylip_CheckFileFormat’: ./esl_msafile_phylip.c:687:13: note: ‘nres1’ was declared here 687 | int nres1; | ^~~~~ In function ‘phylip_deduce_namewidth’, inlined from ‘phylip_check_interleaved’ at ./esl_msafile_phylip.c:747:22, inlined from ‘esl_msafile_phylip_CheckFileFormat’ at ./esl_msafile_phylip.c:389:13: ./esl_msafile_phylip.c:1048:10: warning: ‘ncols0’ may be used uninitialized [-Wmaybe-uninitialized] 1048 | for (c = ncols0-1; nres1 && c >= 0; c--) | ~~^~~~~~~~~~ ./esl_msafile_phylip.c: In function ‘esl_msafile_phylip_CheckFileFormat’: ./esl_msafile_phylip.c:683:20: note: ‘ncols0’ was declared here 683 | int ncols, ncols0; | ^~~~~~ GEN esl_msafile_psiblast_utest GEN esl_msafile_selex_utest GEN esl_msafile_stockholm_utest GEN esl_msaweight_utest ./esl_msaweight.c: In function ‘esl_msaweight_IDFilter_adv’: ./esl_msaweight.c:1035:9: warning: ‘conscols_103’ may be used uninitialized [-Wmaybe-uninitialized] 1035 | collect_counts(cfg, msa, conscols, ncons, ct, NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./esl_msaweight.c:435:1: note: by argument 3 of type ‘const int *’ to ‘collect_counts.isra.0’ declared here 435 | collect_counts(const ESL_MSAWEIGHT_CFG *cfg, const ESL_MSA *msa, const int *conscols, int ncons, int **ct, ESL_MSAWEIGHT_DAT *dat) | ^~~~~~~~~~~~~~ GEN esl_normal_utest GEN esl_quicksort_utest GEN esl_random_utest GEN esl_rand64_utest GEN esl_randomseq_utest GEN esl_ratematrix_utest GEN esl_red_black_utest In function ‘esl_red_black_doublekey_linked_list_test’, inlined from ‘main’ at ./esl_red_black.c:702:8: ./esl_red_black.c:563:5: warning: ‘prev’ may be used uninitialized [-Wmaybe-uninitialized] 563 | if(prev != head_ptr){ | ^ ./esl_red_black.c: In function ‘main’: ./esl_red_black.c:546:28: note: ‘prev’ was declared here 546 | ESL_RED_BLACK_DOUBLEKEY *prev; | ^~~~ GEN esl_recorder_utest GEN esl_regexp_utest GEN esl_rootfinder_utest GEN esl_scorematrix_utest In file included from ./esl_scorematrix.c:22: ./esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ./easel.h:164:17: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 164 | if ( ((p) = malloc(size)) == NULL) { \ | ^~~~~~~~~~~~ In file included from ./easel.h:21: /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ ./esl_scorematrix.c: In function ‘esl_scorematrix_Create’: ./esl_scorematrix.c:71:3: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 71 | ESL_ALLOC(S->outorder, sizeof(char) * (abc->Kp+1)); | ^ /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^ GEN esl_sq_utest In function ‘esl_sq_DestroyBlock’, inlined from ‘esl_sq_DestroyBlock’ at ./esl_sq.c:583:1, inlined from ‘sq_createblock’ at ./esl_sq.c:2152:3: ./esl_sq.c:589:24: warning: ‘block_15->listSize’ may be used uninitialized [-Wmaybe-uninitialized] 589 | for (i = 0; i < block->listSize; ++i) | ~~~~~^~~~~~~~~~ ./esl_sq.c:589:24: warning: ‘block_15->listSize’ may be used uninitialized [-Wmaybe-uninitialized] GEN esl_sqio_utest GEN esl_ssi_utest GEN esl_stack_utest GEN esl_stats_utest GEN esl_stretchexp_utest GEN esl_tree_utest GEN esl_varint_utest ./esl_varint.c: In function ‘esl_varint_google_decode’: ./esl_varint.c:474:11: warning: ‘grp’ may be used uninitialized [-Wmaybe-uninitialized] 474 | if (grp & cmask) { status = eslEOD; goto ERROR; } | ~~~~^~~~~~~ ./esl_varint.c:464:12: note: ‘grp’ was declared here 464 | uint64_t grp; // current k-bit code group | ^~~ GEN esl_vectorops_utest GEN esl_weibull_utest GEN esl_wuss_utest ./esl_wuss.c: In function ‘esl_wuss2ct’: ./esl_wuss.c:136:10: warning: ‘status’ may be used uninitialized [-Wmaybe-uninitialized] 136 | return status; | ^~~~~~ ./esl_wuss.c:56:14: note: ‘status’ was declared here 56 | int status; /* success or failure return status */ | ^~~~~~ GEN esl_sse_utest GEN esl_avx_utest GEN esl_avx512_utest GEN esl_neon_utest GEN esl_vmx_utest SUBDIR miniapps SUBDIR libdivsufsort SUBDIR src SUBDIR impl_sse GEN build_utest GEN generic_fwdback_utest GEN generic_fwdback_chk_utest GEN generic_msv_utest GEN generic_stotrace_utest ./generic_stotrace.c: In function ‘p7_GStochasticTrace’: ./generic_stotrace.c:172:21: warning: ‘scur’ may be used uninitialized [-Wmaybe-uninitialized] 172 | if ((status = p7_trace_Append(tr, scur, k, i)) != eslOK) goto ERROR; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./generic_stotrace.c:57:11: note: ‘scur’ was declared here 57 | int scur, sprv; | ^~~~ GEN generic_viterbi_utest GEN hmmer_utest GEN logsum_utest GEN modelconfig_utest GEN seqmodel_utest GEN p7_alidisplay_utest GEN p7_bg_utest GEN p7_domain_utest ./p7_domain.c: In function ‘p7_domain_Serialize’: ./p7_domain.c:191:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 191 | network_32bit = esl_hton32(*((uint32_t *) &(obj->envsc))); // ow, this hurts, but is probably the best way to get the | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_domain.c:198:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 198 | network_32bit = esl_hton32(*((uint32_t *) &(obj->domcorrection))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_domain.c:203:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 203 | network_32bit = esl_hton32(*((uint32_t *) &(obj->dombias))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_domain.c:208:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 208 | network_32bit = esl_hton32(*((uint32_t *) &(obj->oasc))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_domain.c:213:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 213 | network_32bit = esl_hton32(*((uint32_t *) &(obj->bitscore))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_domain.c:218:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 218 | network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_domain.c: In function ‘p7_domain_Deserialize’: ./p7_domain.c:341:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 341 | ret_obj->envsc = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ ./p7_domain.c:347:30: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 347 | ret_obj->domcorrection = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ ./p7_domain.c:353:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 353 | ret_obj->dombias = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ ./p7_domain.c:359:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 359 | ret_obj->oasc = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ ./p7_domain.c:365:25: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 365 | ret_obj->bitscore = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ ./p7_domain.c:371:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 371 | ret_obj->lnP = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ ./p7_domain.c:398:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 398 | ret_obj->scores_per_pos[i] = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ GEN p7_gmx_utest GEN p7_gmxchk_utest GEN p7_hit_utest ./p7_hit.c: In function ‘p7_hit_Serialize’: ./p7_hit.c:226:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 226 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sortkey))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:231:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 231 | network_32bit = esl_hton32(*((uint32_t *) &(obj->score))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:236:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 236 | network_32bit = esl_hton32(*((uint32_t *) &(obj->pre_score))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:241:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 241 | network_32bit = esl_hton32(*((uint32_t *) &(obj->sum_score))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:246:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 246 | network_64bit = esl_hton64(*((uint64_t *) &(obj->lnP))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:251:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 251 | network_64bit = esl_hton64(*((uint64_t *) &(obj->pre_lnP))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:256:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 256 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sum_lnP))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:261:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 261 | network_32bit = esl_hton32(*((uint32_t *) &(obj->nexpected))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c: In function ‘p7_hit_Deserialize’: ./p7_hit.c:408:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 408 | ret_obj->sortkey = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:414:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 414 | ret_obj->score = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:420:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 420 | ret_obj->pre_score = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:426:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 426 | ret_obj->sum_score = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:432:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 432 | ret_obj->lnP = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:438:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 438 | ret_obj->pre_lnP = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:444:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 444 | ret_obj->sum_lnP = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ ./p7_hit.c:450:26: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 450 | ret_obj->nexpected = *((float *) &host_32bit); | ~^~~~~~~~~~~~~~~~~~~~~~ GEN p7_hmmd_search_stats_utest ./p7_hmmd_search_stats.c: In function ‘p7_hmmd_search_stats_Serialize’: ./p7_hmmd_search_stats.c:89:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 89 | network_64bit = esl_hton64(*((uint64_t *) &(obj->elapsed))); // ow, this hurts, but is probably the best way to get the | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_hmmd_search_stats.c:97:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 97 | network_64bit = esl_hton64(*((uint64_t *) &(obj->user))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_hmmd_search_stats.c:103:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 103 | network_64bit = esl_hton64(*((uint64_t *) &(obj->sys))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_hmmd_search_stats.c:109:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 109 | network_64bit = esl_hton64(*((uint64_t *) &(obj->Z))); | ~^~~~~~~~~~~~~~~~~~~~~~~ ./p7_hmmd_search_stats.c:115:32: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 115 | network_64bit = esl_hton64(*((uint64_t *) &(obj->domZ))); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_hmmd_search_stats.c: In function ‘p7_hmmd_search_stats_Deserialize’: ./p7_hmmd_search_stats.c:256:24: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 256 | ret_obj->elapsed = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ ./p7_hmmd_search_stats.c:262:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 262 | ret_obj->user = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ ./p7_hmmd_search_stats.c:268:20: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 268 | ret_obj->sys = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ ./p7_hmmd_search_stats.c:274:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 274 | ret_obj->Z = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ ./p7_hmmd_search_stats.c:280:21: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 280 | ret_obj->domZ = *((double *) &host_64bit); | ~^~~~~~~~~~~~~~~~~~~~~~~ GEN p7_hmm_utest GEN p7_hmmfile_utest GEN p7_profile_utest GEN p7_tophits_utest In file included from /usr/include/stdio.h:970, from ../easel/easel.h:22, from ./p7_tophits.c:16: In function ‘fprintf’, inlined from ‘p7_tophits_Targets’ at ./p7_tophits.c:1142:12: /usr/include/bits/stdio2.h:111:10: warning: ‘posw’ may be used uninitialized [-Wmaybe-uninitialized] 111 | return __fprintf_chk (__stream, __USE_FORTIFY_LEVEL - 1, __fmt, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 112 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ ./p7_tophits.c: In function ‘p7_tophits_Targets’: ./p7_tophits.c:1068:10: note: ‘posw’ was declared here 1068 | int posw; | ^~~~ ./p7_tophits.c: In function ‘main’: ./p7_tophits.c:2171:3: warning: ‘key’ may be used uninitialized [-Wmaybe-uninitialized] 2171 | p7_tophits_Add(h1, "last", NULL, NULL, -1.0, (float) key, key, (float) key, key, i, i, N, i, i, N, 1, 1, NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./p7_tophits.c:2155:19: note: ‘key’ was declared here 2155 | double key; | ^~~ GEN p7_trace_utest GEN p7_scoredata_utest GEN hmmpgmd2msa_utest GEN hmmd_search_status_utest CC itest_brute.o GEN itest_brute SUBDIR impl_sse GEN decoding_utest GEN fwdback_utest GEN io_utest GEN msvfilter_utest GEN null2_utest GEN optacc_utest In function ‘get_postprob’, inlined from ‘p7_OATrace’ at ./optacc.c:254:18: ./optacc.c:273:3: warning: ‘smax’ may be used uninitialized [-Wmaybe-uninitialized] 273 | switch (scur) { | ^~~~~~ ./optacc.c: In function ‘p7_OATrace’: ./optacc.c:398:10: note: ‘smax’ was declared here 398 | int smax, kmax; | ^~~~ In function ‘get_postprob’, inlined from ‘p7_OATrace’ at ./optacc.c:254:18: ./optacc.c:269:21: warning: ‘kmax’ may be used uninitialized [-Wmaybe-uninitialized] 269 | int q = (k-1) % Q; /* (q,r) is position of the current DP cell M(i,k) */ | ~~^~~ ./optacc.c: In function ‘p7_OATrace’: ./optacc.c:398:16: note: ‘kmax’ was declared here 398 | int smax, kmax; | ^~~~ GEN stotrace_utest GEN vitfilter_utest SUBDIR easel SUBDIR miniapps SUBDIR testsuite Running Easel test suite... exercise 1 [ easel-utest] ... ok. exercise 2 [ alloc-utest] ... ok. exercise 3 [ alphabet-utest] ... ok. exercise 4 [ avx-utest] ... ok. exercise 5 [ avx512-utest] ... ok. exercise 6 [ bitfield-utest] ... ok. exercise 7 [ buffer-utest] ... ok. exercise 8 [ cluster-utest] ... ok. exercise 9 [ cpu-utest] ... ok. exercise 10 [ dirichlet-utest] ... ok. exercise 11 [ distance-utest] ... ok. exercise 12 [ dmatrix-utest] ... ok. exercise 13 [ dsqdata-utest] ... ok. exercise 14 [ exponential-utest] ... ok. exercise 15 [ fileparser-utest] ... ok. exercise 16 [ gamma-utest] ... ok. exercise 17 [ gencode-utest] ... ok. exercise 18 [ getopts-utest] ... ok. exercise 19 [ graph-utest] ... ok. exercise 20 [ gumbel-utest] ... ok. exercise 21 [ heap-utest] ... ok. exercise 22 [ histogram-utest] ... ok. exercise 23 [ huffman-utest] ... ok. exercise 24 [ hyperexp-utest] ... ok. exercise 25 [ json-utest] ... ok. exercise 26 [ keyhash-utest] ... ok. exercise 27 [ matrixops-utest] ... ok. exercise 28 [ mem-utest] ... ok. exercise 29 [ minimizer-utest] ... ok. exercise 30 [ mixdchlet-utest] ... ok. exercise 31 [ msa-utest] ... ok. exercise 32 [ msacluster-utest] ... ok. exercise 33 [ msafile] ... ok. exercise 34 [ msafile2] ... ok. exercise 35 [ msafile-a2m] ... ok. exercise 36 [ msafile-afa] ... ok. exercise 37 [ msafile-clustal] ... ok. exercise 38 [ msafile-phylip] ... ok. exercise 39 [ msafile-psiblast] ... ok. exercise 40 [ msafile-selex] ... ok. exercise 41 [ msafile-stockholm] ... ok. exercise 42 [ msaweight-utest] ... ok. exercise 43 [ neon-utest] ... ok. exercise 44 [ normal-utest] ... ok. exercise 45 [ quicksort-utest] ... ok. exercise 46 [ random-utest] ... ok. exercise 47 [ rand64-utest] ... ok. exercise 48 [ randomseq-utest] ... ok. exercise 49 [ ratematrix-utest] ... ok. exercise 50 [ recorder-utest] ... ok. exercise 51 [ red_black-utest] ... ok. exercise 52 [ regexp-utest] ... ok. exercise 53 [ rootfinder-utest] ... ok. exercise 54 [ scorematrix-utest] ... ok. exercise 55 [ sq-utest] ... ok. exercise 56 [ sqio-utest] ... ok. exercise 57 [ sse-utest] ... ok. exercise 58 [ ssi-utest] ... ok. exercise 59 [ stack-utest] ... ok. exercise 60 [ stats-utest] ... ok. exercise 61 [ stretchexp-utest] ... ok. exercise 62 [ tree-utest] ... ok. exercise 63 [ varint-utest] ... ok. exercise 64 [ vectorops-utest] ... ok. exercise 65 [ vmx-utest] ... ok. exercise 66 [ weibull-utest] ... ok. exercise 67 [ wuss-utest] ... ok. exercise 68 [ e2] ... ok. exercise 69 [ degen-residues] ... ok. exercise 70 [ ncbi-indices] ... ok. exercise 71 [ blank-gf] ... ok. exercise 72 [ esl-translate] ... ok. exercise 73 [ esl-afetch] ... ok. exercise 74 [ esl-alimanip] ... ok. exercise 75 [ esl-alimap] ... ok. exercise 76 [ esl-alimask] ... ok. exercise 77 [ esl-alimerge] ... ok. exercise 78 [ esl-alistat] ... ok. exercise 79 [ esl-compalign] ... ok. exercise 80 [ esl-construct] ... ok. exercise 81 [ esl-mask] ... ok. exercise 82 [ esl-seqrange] ... ok. exercise 83 [ esl-shuffle] ... ok. exercise 84 [ esl-ssdraw] ... ok. All 84 exercises at level <= 2 passed. System information: Tue Oct 7 18:16:53 UTC 2025 Linux 02f6e607abb74525bcdbd6ed5a7ea75e 6.16.7-200.fc42.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Sep 11 17:46:54 UTC 2025 x86_64 GNU/Linux SUBDIR testsuite Running HMMER test suite... exercise 1 [ hmmer] ... ok. exercise 2 [ build] ... ok. exercise 3 [ generic_fwdback] ... ok. exercise 4 [ generic_msv] ... ok. exercise 5 [ generic_stotrace] ... ok. exercise 6 [ generic_viterbi] ... ok. exercise 7 [ hmmd_search_status] ... ok. exercise 8 [ logsum] ... ok. exercise 9 [ modelconfig] ... ok. exercise 10 [ seqmodel] ... ok. exercise 11 [ p7_alidisplay] ... ok. exercise 12 [ p7_bg] ... ok. exercise 13 [ p7_domain] ... ok. exercise 14 [ p7_gmx] ... ok. exercise 15 [ p7_hit] ... ok. exercise 16 [ p7_hmm] ... ok. exercise 17 [ p7_hmmfile] ... ok. exercise 18 [ p7_hmmd_search_stats] ... ok. exercise 19 [ p7_profile] ... ok. exercise 20 [ p7_tophits] ... ok. exercise 21 [ p7_trace] ... ok. exercise 22 [ p7_scoredata] ... ok. exercise 23 [ decoding] ... ok. exercise 24 [ fwdback] ... ok. exercise 25 [ io] ... ok. exercise 26 [ msvfilter] ... ok. exercise 27 [ null2] ... ok. exercise 28 [ optacc] ... ok. exercise 29 [ stotrace] ... ok. exercise 30 [ vitfilter] ... ok. exercise 31 [ hmmpgmd2msa] ... ok. exercise 32 [ hmmalign] ... ok. exercise 33 [ hmmalign/-h] ... ok. exercise 34 [ hmmalign/-o] ... ok. exercise 35 [ hmmalign/--mapali] ... ok. exercise 36 [ hmmalign/--trim] ... ok. exercise 37 [ hmmalign/--amino] ... ok. exercise 38 [ hmmalign/--informat] ... ok. exercise 39 [ hmmalign/--outformat] ... ok. exercise 40 [ hmmbuild] ... ok. exercise 41 [ build/-h] ... ok. exercise 42 [ build/-n] ... ok. exercise 43 [ build/-o] ... ok. exercise 44 [ build/-O] ... ok. exercise 45 [ build/--amino] ... ok. exercise 46 [ build/--dna] ... ok. exercise 47 [ build/--rna] ... ok. exercise 48 [ build/--fast] ... ok. exercise 49 [ build/--hand] ... ok. exercise 50 [ build/--symfrac] ... ok. exercise 51 [ build/--fragthresh] ... ok. exercise 52 [ build/--wpb] ... ok. exercise 53 [ build/--wgsc] ... ok. exercise 54 [ build/--wblosum] ... ok. exercise 55 [ build/--wnone] ... ok. exercise 56 [ build/--wid] ... ok. exercise 57 [ build/--eent] ... ok. exercise 58 [ build/--eclust] ... ok. exercise 59 [ build/--enone] ... ok. exercise 60 [ build/--eset] ... ok. exercise 61 [ build/--ere] ... ok. exercise 62 [ build/--esigma] ... ok. exercise 63 [ build/--eid] ... ok. exercise 64 [ build/--pnone] ... ok. exercise 65 [ build/--plaplace] ... ok. exercise 66 [ build/--EmL] ... ok. exercise 67 [ build/--EmN] ... ok. exercise 68 [ build/--EvL] ... ok. exercise 69 [ build/--EvN] ... ok. exercise 70 [ build/--EfL] ... ok. exercise 71 [ build/--EfN] ... ok. exercise 72 [ build/--Eft] ... ok. exercise 73 [ build/--informat] ... ok. exercise 74 [ build/--seed] ... ok. exercise 75 [ search] ... ok. exercise 76 [ search/-h] ... ok. exercise 77 [ search/-o] ... ok. exercise 78 [ search/-A] ... ok. exercise 79 [ search/--tblout] ... ok. exercise 80 [ search/--domtblout] ... ok. exercise 81 [ search/--pfamtblout] ... ok. exercise 82 [ search/--acc] ... ok. exercise 83 [ search/--noali] ... ok. exercise 84 [ search/--notextw] ... ok. exercise 85 [ search/--textw] ... ok. exercise 86 [ search/-E] ... ok. exercise 87 [ search/-T] ... ok. exercise 88 [ search/--domE] ... ok. exercise 89 [ search/--domT] ... ok. exercise 90 [ search/--incE] ... ok. exercise 91 [ search/--incT] ... ok. exercise 92 [ search/--incdomE] ... ok. exercise 93 [ search/--incdomT] ... ok. exercise 94 [ search/--cut_ga] ... ok. exercise 95 [ search/--cut_nc] ... ok. exercise 96 [ search/--cut_tc] ... ok. exercise 97 [ search/--max] ... ok. exercise 98 [ search/--F1] ... ok. exercise 99 [ search/--F2] ... ok. exercise 100 [ search/--F3] ... ok. exercise 101 [ search/--nobias] ... ok. exercise 102 [ search/--nonull2] ... ok. exercise 103 [ search/-Z] ... ok. exercise 104 [ search/--domZ] ... ok. exercise 105 [ search/--seed] ... ok. exercise 106 [ search/--tformat] ... ok. exercise 107 [ hmmscan] ... ok. exercise 108 [ scan/-h] ... ok. exercise 109 [ scan/-o] ... ok. exercise 110 [ scan/--tblout] ... ok. exercise 111 [ scan/--domtblout] ... ok. exercise 112 [ scan/--pfamtblout] ... ok. exercise 113 [ scan/--acc] ... ok. exercise 114 [ scan/--noali] ... ok. exercise 115 [ scan/--notextw] ... ok. exercise 116 [ scan/--textw] ... ok. exercise 117 [ scan/-E] ... ok. exercise 118 [ scan/-T] ... ok. exercise 119 [ scan/--domE] ... ok. exercise 120 [ scan/--domT] ... ok. exercise 121 [ scan/--incE] ... ok. exercise 122 [ scan/--incT] ... ok. exercise 123 [ scan/--incdomE] ... ok. exercise 124 [ scan/--incdomT] ... ok. exercise 125 [ scan/--incdomT] ... ok. exercise 126 [ scan/--cut_ga] ... ok. exercise 127 [ scan/--cut_nc] ... ok. exercise 128 [ scan/--cut_tc] ... ok. exercise 129 [ scan/--max] ... ok. exercise 130 [ scan/--F1] ... ok. exercise 131 [ scan/--F2] ... ok. exercise 132 [ scan/--F3] ... ok. exercise 133 [ scan/--nobias] ... ok. exercise 134 [ scan/--nonull2] ... ok. exercise 135 [ scan/-Z] ... ok. exercise 136 [ scan/--domZ] ... ok. exercise 137 [ scan/--seed] ... ok. exercise 138 [ scan/--qformat] ... ok. exercise 139 [ scan/--cpu] ... ok. exercise 140 [ jackhmmer] ... ok. exercise 141 [ j/-h] ... ok. exercise 142 [ j/-N] ... ok. exercise 143 [ j/-o] ... ok. exercise 144 [ j/-A] ... ok. exercise 145 [ j/--tblout] ... ok. exercise 146 [ j/--domtblout] ... ok. exercise 147 [ j/--chkhmm] ... ok. exercise 148 [ j/--chkali] ... ok. exercise 149 [ j/--acc] ... ok. exercise 150 [ j/--noali] ... ok. exercise 151 [ j/--notextw] ... ok. exercise 152 [ j/--textw] ... ok. exercise 153 [ j/--popen] ... ok. exercise 154 [ j/--pextend] ... ok. exercise 155 [ j/--mxfile] ... ok. exercise 156 [ j/-E] ... ok. exercise 157 [ j/-T] ... ok. exercise 158 [ j/--domE] ... ok. exercise 159 [ j/--domT] ... ok. exercise 160 [ j/--incE] ... ok. exercise 161 [ j/--incT] ... ok. exercise 162 [ j/--incdomE] ... ok. exercise 163 [ j/--incdomT] ... ok. exercise 164 [ j/--max] ... ok. exercise 165 [ j/--F1] ... ok. exercise 166 [ j/--F2] ... ok. exercise 167 [ j/--F3] ... ok. exercise 168 [ j/--nobias] ... ok. exercise 169 [ j/--EmL] ... ok. exercise 170 [ j/--EmN] ... ok. exercise 171 [ j/--EvL] ... ok. exercise 172 [ j/--EvN] ... ok. exercise 173 [ j/--EfL] ... ok. exercise 174 [ j/--EfN] ... ok. exercise 175 [ j/--Eft] ... ok. exercise 176 [ j/--nonull2] ... ok. exercise 177 [ j/-Z] ... ok. exercise 178 [ j/--domZ] ... ok. exercise 179 [ j/--seed] ... ok. exercise 180 [ j/--qformat] ... ok. exercise 181 [ j/--tformat] ... ok. exercise 182 [ phmmer] ... ok. exercise 183 [ phmmer/-h] ... ok. exercise 184 [ phmmer/-o] ... ok. exercise 185 [ phmmer/-A] ... ok. exercise 186 [ phmmer/--tblout] ... ok. exercise 187 [ phmmer/--domtblout] ... ok. exercise 188 [ phmmer/--pfamtblout] ... ok. exercise 189 [ phmmer/--acc] ... ok. exercise 190 [ phmmer/--noali] ... ok. exercise 191 [ phmmer/--notextw] ... ok. exercise 192 [ phmmer/--textw] ... ok. exercise 193 [ phmmer/--popen] ... ok. exercise 194 [ phmmer/--pextend] ... ok. exercise 195 [ phmmer/--mxfile] ... ok. exercise 196 [ phmmer/-E] ... ok. exercise 197 [ phmmer/-T] ... ok. exercise 198 [ phmmer/--domE] ... ok. exercise 199 [ phmmer/--domT] ... ok. exercise 200 [ phmmer/--incE] ... ok. exercise 201 [ phmmer/--incT] ... ok. exercise 202 [ phmmer/--incdomE] ... ok. exercise 203 [ phmmer/--incdomT] ... ok. exercise 204 [ phmmer/--max] ... ok. exercise 205 [ phmmer/--F1] ... ok. exercise 206 [ phmmer/--F2] ... ok. exercise 207 [ phmmer/--F3] ... ok. exercise 208 [ phmmer/--nobias] ... ok. exercise 209 [ phmmer/--EmL] ... ok. exercise 210 [ phmmer/--EmN] ... ok. exercise 211 [ phmmer/--EvL] ... ok. exercise 212 [ phmmer/--EvN] ... ok. exercise 213 [ phmmer/--EfL] ... ok. exercise 214 [ phmmer/--EfN] ... ok. exercise 215 [ phmmer/--Eft] ... ok. exercise 216 [ phmmer/--nonull2] ... ok. exercise 217 [ phmmer/-Z] ... ok. exercise 218 [ phmmer/--domZ] ... ok. exercise 219 [ phmmer/--seed] ... ok. exercise 220 [ phmmer/--qformat] ... ok. exercise 221 [ phmmer/--tformat] ... ok. exercise 222 [ nhmmer] ... ok. exercise 223 [ nhmmer/-h] ... ok. exercise 224 [ nhmmer/-o] ... ok. exercise 225 [ nhmmer/-A] ... ok. exercise 226 [ nhmmer/--tblout] ... ok. exercise 227 [ nhmmer/--dfamtblout] ... ok. exercise 228 [ nhmmer/--acc] ... ok. exercise 229 [ nhmmer/--noali] ... ok. exercise 230 [ nhmmer/--notextw] ... ok. exercise 231 [ nhmmer/--textw] ... ok. exercise 232 [ nhmmer/-E] ... ok. exercise 233 [ nhmmer/-T] ... ok. exercise 234 [ nhmmer/--incE] ... ok. exercise 235 [ nhmmer/--incT] ... ok. exercise 236 [ nhmmer/--max] ... ok. exercise 237 [ nhmmer/--F1] ... ok. exercise 238 [ nhmmer/--F2] ... ok. exercise 239 [ nhmmer/--F3] ... ok. exercise 240 [ nhmmer/--nobias] ... ok. exercise 241 [ nhmmer/--nonull2] ... ok. exercise 242 [ nhmmer/-Z] ... ok. exercise 243 [ nhmmer/--seed] ... ok. exercise 244 [ nhmmscan] ... ok. exercise 245 [ nhmmscan/-h] ... ok. exercise 246 [ nhmmscan/-o] ... ok. exercise 247 [ nhmmscan/--tblout] ... ok. exercise 248 [nhmmscan/--dfamtblout] ... ok. exercise 249 [ nhmmscan/--acc] ... ok. exercise 250 [ nhmmscan/--noali] ... ok. exercise 251 [ nhmmscan/--notextw] ... ok. exercise 252 [ nhmmscan/--textw] ... ok. exercise 253 [ nhmmscan/-E] ... ok. exercise 254 [ nhmmscan/-T] ... ok. exercise 255 [ nhmmscan/--incE] ... ok. exercise 256 [ nhmmscan/--incT] ... ok. exercise 257 [ nhmmscan/--max] ... ok. exercise 258 [ nhmmscan/--F1] ... ok. exercise 259 [ nhmmscan/--F2] ... ok. exercise 260 [ nhmmscan/--F3] ... ok. exercise 261 [ nhmmscan/--nobias] ... ok. exercise 262 [ nhmmscan/--nonull2] ... ok. exercise 263 [ nhmmscan/-Z] ... ok. exercise 264 [ nhmmscan/--seed] ... ok. exercise 265 [ hmmemit] ... ok. exercise 266 [ hmmemit/-h] ... ok. exercise 267 [ hmmemit/-c] ... ok. exercise 268 [ hmmemit/-o] ... ok. exercise 269 [ hmmemit/-p] ... ok. exercise 270 [ hmmemit/-N] ... ok. exercise 271 [ hmmemit/-L] ... ok. exercise 272 [ hmmemit/--local] ... ok. exercise 273 [ hmmemit/--unilocal] ... ok. exercise 274 [ hmmemit/--glocal] ... ok. exercise 275 [ hmmemit/--uniglocal] ... ok. exercise 276 [ hmmfetch] ... ok. exercise 277 [ hmmstat] ... ok. exercise 278 [ hmmlogo] ... ok. exercise 279 [ hmmconvert] ... ok. exercise 280 [ hmmsim] ... ok. exercise 281 [ hmmbuild_variation] ... ok. exercise 282 [ hmmscan_variation] ... ok. exercise 283 [ hmmsearch_variation] ... ok. exercise 284 [ phmmer_variation] ... ok. exercise 285 [ mapali] ... ok. exercise 286 [ fragments] ... ok. exercise 287 [ nonresidues] ... ok. exercise 288 [ opt-annotation] ... ok. exercise 289 [ dup-names] ... ok. exercise 290 [ mapali-again] ... ok. exercise 291 [ delete-corruption] ... ok. exercise 292 [ msa-integrity] ... ok. exercise 293 [ hmmemit-consensus] ... ok. exercise 294 [ hmmconvert] ... ok. exercise 295 [ stdin_pipes] ... ok. exercise 296 [ nhmmer_generic] ... ok. exercise 297 [ hmmpgmd_ga] ... ok. exercise 298 [ rewind] ... ok. exercise 299 [ hmmpgmd_shard_ga] ... ok. exercise 300 [ bad-fasta] ... ok. exercise 301 [ brute-itest] ... ok. exercise 302 [ hmmpress-itest] ... ok. exercise 303 [ h39] ... ok. exercise 304 [ h45] ... ok. exercise 305 [ h50] ... ok. exercise 306 [ h82] ... ok. exercise 307 [ iss159] ... ok. All 307 exercises at level <= 2 passed. System information: Tue Oct 7 18:17:05 UTC 2025 Linux 02f6e607abb74525bcdbd6ed5a7ea75e 6.16.7-200.fc42.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Sep 11 17:46:54 UTC 2025 x86_64 GNU/Linux + RPM_EC=0 ++ jobs -p + exit 0 Processing files: hmmer-3.3.2-11.fc44.x86_64 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.nQTu83 + umask 022 + cd /builddir/build/BUILD/hmmer-3.3.2-build + cd hmmer-3.3.2 + LICENSEDIR=/builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/licenses/hmmer + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/licenses/hmmer + cp -pr /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/LICENSE /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/licenses/hmmer + RPM_EC=0 ++ jobs -p + exit 0 Provides: hmmer = 3.3.2-11.fc44 hmmer(x86-64) = 3.3.2-11.fc44 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.11)(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.15)(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.27)(64bit) libm.so.6(GLIBC_2.29)(64bit) rtld(GNU_HASH) Processing files: hmmer-easel-3.3.2-11.fc44.x86_64 Provides: hmmer-easel = 3.3.2-11.fc44 hmmer-easel(x86-64) = 3.3.2-11.fc44 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) rtld(GNU_HASH) Processing files: hmmer-doc-3.3.2-11.fc44.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.CI3Okz + umask 022 + cd /builddir/build/BUILD/hmmer-3.3.2-build + cd hmmer-3.3.2 + DOCDIR=/builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc + cp -pr /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/LICENSE /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc + cp -pr /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/README.md /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc + cp -pr /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/RELEASE-3.3.2.md /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc + cp -pr /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/Userguide.pdf /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc + cp -pr /builddir/build/BUILD/hmmer-3.3.2-build/hmmer-3.3.2/tutorial /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT/usr/share/doc/hmmer-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: hmmer-doc = 3.3.2-11.fc44 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: hmmer-debugsource-3.3.2-11.fc44.x86_64 Provides: hmmer-debugsource = 3.3.2-11.fc44 hmmer-debugsource(x86-64) = 3.3.2-11.fc44 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: hmmer-debuginfo-3.3.2-11.fc44.x86_64 Provides: debuginfo(build-id) = 0cb1704dcae823bed1ba14f549abbf2e752f8c1d debuginfo(build-id) = 1ba988b93b6887a701ffda36e240cc1bc624acb0 debuginfo(build-id) = 1c801c776eaf54b82a63fa4946554824a867fecb debuginfo(build-id) = 283d171f27fb9f6be486842d287912126d3c045d debuginfo(build-id) = 2d9b19273b5bf8050cbe8b76385ef2889985a42b debuginfo(build-id) = 30e9a08988e751e4041fe0cd21c06fadd5f1537f debuginfo(build-id) = 39d1860cdc7ea3904dcf6f7a164f472dd9ac3f0b debuginfo(build-id) = 7618da2f224b5c7b0622b833a3246a4e45ec15f9 debuginfo(build-id) = 8181ea9fd56c03f939b5ef898b142d2454125ae0 debuginfo(build-id) = 8feec4e62262e6da0f762d610fb28f6b6c46d347 debuginfo(build-id) = 90d4e6a0ec74d8e75ec03ea5bd53f3889af417a6 debuginfo(build-id) = 96cf71ed79d6d6f8026f8c893fb79ea47205fdbe debuginfo(build-id) = 96eb0252323b7b18b7de66131d99d70f18f8f40c debuginfo(build-id) = b04d132f9f9891684701b29ef0c27464471d5870 debuginfo(build-id) = bcc032c98001cc0b673cbec514aa4a3ed948623b debuginfo(build-id) = c15c052ec38bf3495b2f4c6f489634785747c9a9 debuginfo(build-id) = c660ae267a40c30b1ff8a45b5d5f839f3d9488f9 debuginfo(build-id) = e8d4049ff9b2597410d8e7ae24850d081d85ee98 debuginfo(build-id) = f81b1ba53e07471d1f7ea3c719e3a2c2786f9636 hmmer-debuginfo = 3.3.2-11.fc44 hmmer-debuginfo(x86-64) = 3.3.2-11.fc44 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: hmmer-debugsource(x86-64) = 3.3.2-11.fc44 Processing files: hmmer-easel-debuginfo-3.3.2-11.fc44.x86_64 Provides: debuginfo(build-id) = 18ff3e8f6ec45db208d2aeca4ce33285d921e99c debuginfo(build-id) = 192cce3758f17189342ec16ced5c305ca2be68a3 debuginfo(build-id) = 233a32329f296bbbf488dff9d26682d578edfa0e debuginfo(build-id) = 27492c9a03a8820025c846416d81be1d64d454c5 debuginfo(build-id) = 2eb71c6b05975dfd745d704b9cc9fdf5538a8cdd debuginfo(build-id) = 40eb1f4ec6eb3967c9b0eb06ed18bf6e8564cfcb debuginfo(build-id) = 57d048841d28fa8a1b32d7185a4d008b0dad11e8 debuginfo(build-id) = 584d852c7764fe2e0945e206a648eb93c817a1e4 debuginfo(build-id) = 62fc84778fe41099f3a13ee3e2b093b9b6107fe9 debuginfo(build-id) = 69a34062b639be1d17ad7ea6a146f0b6a8aebc06 debuginfo(build-id) = 7b7f0c8b8eb8bb22d44dc5144eb52513b739e939 debuginfo(build-id) = 82f82bc049bdc033a6f8dfab4445e223102f63b4 debuginfo(build-id) = 914b682b713e38d12559a50e36cc7b51c1d9f4a9 debuginfo(build-id) = 9618229bd4f65e1e6e2363374e288c0835d5a4bc debuginfo(build-id) = aa2b22700ec620136c709fcb7d9de958362c0ae4 debuginfo(build-id) = abe581e67f6dc8f04e690ff145f4b6575f91365f debuginfo(build-id) = b8745652e122a75081fccf8833525404ab0de13c debuginfo(build-id) = bd9a40f108cca6aaab099f3ff837ac972a59ab98 debuginfo(build-id) = d3e63be02c4e79a8886b9d1259f4f260c0485fc5 debuginfo(build-id) = d4109b13ee16e06a09c758e714e0b8c5823bb85f debuginfo(build-id) = e0139357c846c14d2d91665eb1a894a246c5d771 debuginfo(build-id) = f0232e0e6e2336caab79fa32a2ca880c7674d698 debuginfo(build-id) = f209c2c6027b6601ebc39a0da5c18158001c6f74 debuginfo(build-id) = fc8a5d471993f60a8b8f36ed8c8c76b09159b7be hmmer-easel-debuginfo = 3.3.2-11.fc44 hmmer-easel-debuginfo(x86-64) = 3.3.2-11.fc44 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: hmmer-debugsource(x86-64) = 3.3.2-11.fc44 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/hmmer-3.3.2-build/BUILDROOT Wrote: /builddir/build/RPMS/hmmer-3.3.2-11.fc44.x86_64.rpm Wrote: /builddir/build/RPMS/hmmer-debugsource-3.3.2-11.fc44.x86_64.rpm Wrote: /builddir/build/RPMS/hmmer-doc-3.3.2-11.fc44.noarch.rpm Wrote: /builddir/build/RPMS/hmmer-easel-3.3.2-11.fc44.x86_64.rpm Wrote: /builddir/build/RPMS/hmmer-easel-debuginfo-3.3.2-11.fc44.x86_64.rpm Wrote: /builddir/build/RPMS/hmmer-debuginfo-3.3.2-11.fc44.x86_64.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.DrPmJ1 + umask 022 + cd /builddir/build/BUILD/hmmer-3.3.2-build + test -d /builddir/build/BUILD/hmmer-3.3.2-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/hmmer-3.3.2-build + rm -rf /builddir/build/BUILD/hmmer-3.3.2-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild hmmer-3.3.2-11.fc44.src.rpm Finish: build phase for hmmer-3.3.2-11.fc44.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1759860757.492776/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 INFO: Done(/var/lib/copr-rpmbuild/results/hmmer-3.3.2-11.fc44.src.rpm) Config(child) 4 minutes 19 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "hmmer-easel", "epoch": null, "version": "3.3.2", "release": "11.fc44", "arch": "x86_64" }, { "name": "hmmer-debugsource", "epoch": null, "version": "3.3.2", "release": "11.fc44", "arch": "x86_64" }, { "name": "hmmer", "epoch": null, "version": "3.3.2", "release": "11.fc44", "arch": "src" }, { "name": "hmmer-debuginfo", "epoch": null, "version": "3.3.2", "release": "11.fc44", "arch": "x86_64" }, { "name": "hmmer-doc", "epoch": null, "version": "3.3.2", "release": "11.fc44", "arch": "noarch" }, { "name": "hmmer-easel-debuginfo", "epoch": null, "version": "3.3.2", "release": "11.fc44", "arch": "x86_64" }, { "name": "hmmer", "epoch": null, "version": "3.3.2", "release": "11.fc44", "arch": "x86_64" } ] } RPMResults finished