Warning: Permanently added '54.82.62.183' (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/9956457-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64


Version: 1.6
PID: 49970
Logging PID: 49972
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': True,
 'build_id': 9956457,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '7a6407104f26bc7571a959489e49d4278d973153',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/siddhesh/mbp-gcc-16/mmseq',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'mmseq',
 'package_version': '1.0.11-24',
 'project_dirname': 'mbp-gcc-16',
 'project_name': 'mbp-gcc-16',
 'project_owner': 'siddhesh',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/siddhesh/mbp-gcc-16/fedora-rawhide-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None},
           {'baseurl': 'https://kojipkgs.fedoraproject.org/repos/f44-build-side-124978/latest/$basearch/',
            'id': 'https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch',
            'name': 'Additional repo https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch'}],
 'sandbox': 'siddhesh/mbp-gcc-16--siddhesh',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'storage': 0,
 'submitter': 'siddhesh',
 'tags': [],
 'task_id': '9956457-fedora-rawhide-x86_64',
 'timeout': 115200,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/siddhesh/mbp-gcc-16/mmseq /var/lib/copr-rpmbuild/workspace/workdir-3ja8g1tx/mmseq --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/siddhesh/mbp-gcc-16/mmseq', '/var/lib/copr-rpmbuild/workspace/workdir-3ja8g1tx/mmseq', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-3ja8g1tx/mmseq'...

Running: git checkout 7a6407104f26bc7571a959489e49d4278d973153 --

cmd: ['git', 'checkout', '7a6407104f26bc7571a959489e49d4278d973153', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-3ja8g1tx/mmseq
rc: 0
stdout: 
stderr: Note: switching to '7a6407104f26bc7571a959489e49d4278d973153'.

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 <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 7a64071 automatic import of mmseq

Running: dist-git-client sources

cmd: ['dist-git-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-3ja8g1tx/mmseq
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 1.0.11.zip
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o 1.0.11.zip --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/siddhesh/mbp-gcc-16/mmseq/1.0.11.zip/md5/c727916d339d7a2111523800b621ce2b/1.0.11.zip
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 2781k  100 2781k    0     0   120M      0 --:--:-- --:--:-- --:--:--  123M
INFO: Reading stdout from command: md5sum 1.0.11.zip

tail: /var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-3ja8g1tx/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-3ja8g1tx/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1767054237.482716 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 6.6 starting (python version = 3.13.7, NVR = mock-6.6-1.fc42), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-3ja8g1tx/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-3ja8g1tx/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1767054237.482716 -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-3ja8g1tx/mmseq/mmseq.spec)  Config(fedora-rawhide-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 6.6
INFO: Mock Version: 6.6
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1767054237.482716/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-9e82e987-64fa-4ee5-8c0e-ed90f590d021
INFO: Checking that 9ff482f4f7f7693c5a78170426a8e50d75089789bb28676174c922f0ca44a475 image matches host's architecture
INFO: Copy content of container 9ff482f4f7f7693c5a78170426a8e50d75089789bb28676174c922f0ca44a475 to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1767054237.482716/root
INFO: mounting 9ff482f4f7f7693c5a78170426a8e50d75089789bb28676174c922f0ca44a475 with podman image mount
INFO: image 9ff482f4f7f7693c5a78170426a8e50d75089789bb28676174c922f0ca44a475 as /var/lib/containers/storage/overlay/5f8a4f016c15032fb6d9e1fe2849f0952e6cdb3c541438001d8a85a725a39773/merged
INFO: umounting image 9ff482f4f7f7693c5a78170426a8e50d75089789bb28676174c922f0ca44a475 (/var/lib/containers/storage/overlay/5f8a4f016c15032fb6d9e1fe2849f0952e6cdb3c541438001d8a85a725a39773/merged) with podman image umount
INFO: Removing image mock-bootstrap-9e82e987-64fa-4ee5-8c0e-ed90f590d021
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_64-1767054237.482716/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-6.0.1-1.fc44.x86_64
  rpm-sequoia-1.10.0-1.fc44.x86_64
  dnf5-5.3.0.0-3.fc44.x86_64
  dnf5-plugins-5.3.0.0-3.fc44.x86_64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 Additional repo https_kojipkgs_fedorap 100% |  77.7 KiB/s |   3.5 KiB |  00m00s
 Copr repository                        100% |  34.2 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% | 157.0 KiB/s |  30.6 KiB |  00m00s
Repositories loaded.
Package                            Arch   Version                      Repository                                                                        Size
Installing group/module packages:
 bash                              x86_64 0:5.3.0-2.fc44               copr_base                                                                      8.5 MiB
 bzip2                             x86_64 0:1.0.8-21.fc44              copr_base                                                                     95.0 KiB
 coreutils                         x86_64 0:9.9-1.fc44                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   5.4 MiB
 cpio                              x86_64 0:2.15-6.fc44                copr_base                                                                      1.1 MiB
 diffutils                         x86_64 0:3.12-3.fc44                copr_base                                                                      1.6 MiB
 fedora-release-common             noarch 0:44-0.10                    https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  20.6 KiB
 findutils                         x86_64 1:4.10.0-6.fc44              copr_base                                                                      1.9 MiB
 gawk                              x86_64 0:5.3.2-2.fc44               copr_base                                                                      1.8 MiB
 glibc-minimal-langpack            x86_64 0:2.42.9000-17.fc44          fedora                                                                         0.0   B
 grep                              x86_64 0:3.12-2.fc44                copr_base                                                                      1.0 MiB
 gzip                              x86_64 0:1.14-1.fc44                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 397.8 KiB
 info                              x86_64 0:7.2-7.fc44                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 357.9 KiB
 patch                             x86_64 0:2.8-3.fc44                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 226.6 KiB
 redhat-rpm-config                 noarch 0:343-19.fc44                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 183.6 KiB
 rpm-build                         x86_64 0:6.0.1-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 287.5 KiB
 sed                               x86_64 0:4.9-6.fc44                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 857.3 KiB
 shadow-utils                      x86_64 2:4.18.0-7.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   3.9 MiB
 tar                               x86_64 2:1.35-6.fc43                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.9 MiB
 unzip                             x86_64 0:6.0-68.fc44                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 390.3 KiB
 util-linux                        x86_64 0:2.41.3-8.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   3.5 MiB
 which                             x86_64 0:2.23-3.fc43                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  83.5 KiB
 xz                                x86_64 1:5.8.1-4.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.3 MiB
Installing dependencies:
 R-srpm-macros                     noarch 0:1.3.0-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   3.2 KiB
 add-determinism                   x86_64 0:0.7.2-2.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.3 MiB
 alternatives                      x86_64 0:1.33-3.fc44                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  62.2 KiB
 ansible-srpm-macros               noarch 0:1-18.1.fc43                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  35.7 KiB
 audit-libs                        x86_64 0:4.1.2-2.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 378.8 KiB
 binutils                          x86_64 0:2.45.50-12.fc44            copr_base                                                                     27.4 MiB
 build-reproducibility-srpm-macros noarch 0:0.7.2-2.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.2 KiB
 bzip2-libs                        x86_64 0:1.0.8-21.fc44              copr_base                                                                     80.5 KiB
 ca-certificates                   noarch 0:2025.2.80_v9.0.304-2.fc44  https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.7 MiB
 cmake-srpm-macros                 noarch 0:3.31.10-3.fc44             https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 524.0   B
 coreutils-common                  x86_64 0:9.9-1.fc44                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  11.2 MiB
 crypto-policies                   noarch 0:20251128-1.git19878fe.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 132.6 KiB
 curl                              x86_64 0:8.18.0~rc2-1.fc44          https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 471.5 KiB
 cyrus-sasl-lib                    x86_64 0:2.1.28-33.fc44             https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.3 MiB
 debugedit                         x86_64 0:5.2-3.fc44                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 214.0 KiB
 dwz                               x86_64 0:0.16-2.fc44                copr_base                                                                    290.9 KiB
 ed                                x86_64 0:1.22.3-1.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 148.9 KiB
 efi-srpm-macros                   noarch 0:6-5.fc44                   https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  40.2 KiB
 elfutils                          x86_64 0:0.194-2.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.9 MiB
 elfutils-debuginfod-client        x86_64 0:0.194-2.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  84.0 KiB
 elfutils-default-yama-scope       noarch 0:0.194-2.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.8 KiB
 elfutils-libelf                   x86_64 0:0.194-2.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.1 MiB
 elfutils-libs                     x86_64 0:0.194-2.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 687.5 KiB
 fedora-gpg-keys                   noarch 0:44-0.1                     https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 131.2 KiB
 fedora-release                    noarch 0:44-0.10                    https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   0.0   B
 fedora-release-identity-basic     noarch 0:44-0.10                    https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 664.0   B
 fedora-repos                      noarch 0:44-0.1                     https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   4.9 KiB
 fedora-repos-rawhide              noarch 0:44-0.1                     https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.2 KiB
 file                              x86_64 0:5.46-8.fc44                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 100.2 KiB
 file-libs                         x86_64 0:5.46-8.fc44                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  11.9 MiB
 filesystem                        x86_64 0:3.18-51.fc44               copr_base                                                                    112.0   B
 filesystem-srpm-macros            noarch 0:3.18-51.fc44               copr_base                                                                     38.2 KiB
 fonts-srpm-macros                 noarch 1:5.0.0-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  55.8 KiB
 forge-srpm-macros                 noarch 0:0.4.0-3.fc43               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  38.9 KiB
 fpc-srpm-macros                   noarch 0:1.3-15.fc43                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 144.0   B
 gap-srpm-macros                   noarch 0:2-1.fc44                   https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.1 KiB
 gdb-minimal                       x86_64 0:16.3-6.fc44                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  13.3 MiB
 gdbm-libs                         x86_64 1:1.23-10.fc44               copr_base                                                                    129.6 KiB
 ghc-srpm-macros                   noarch 0:1.9.2-3.fc43               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 779.0   B
 glibc                             x86_64 0:2.42.9000-17.fc44          fedora                                                                         6.8 MiB
 glibc-common                      x86_64 0:2.42.9000-17.fc44          fedora                                                                         1.0 MiB
 glibc-gconv-extra                 x86_64 0:2.42.9000-17.fc44          fedora                                                                         7.2 MiB
 gmp                               x86_64 1:6.3.0-4.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 815.3 KiB
 gnat-srpm-macros                  noarch 0:6-8.fc43                   https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.0 KiB
 gnulib-l10n                       noarch 0:20241231-1.fc44            https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 655.0 KiB
 gnupg2                            x86_64 0:2.4.8-4.fc44               copr_base                                                                      6.5 MiB
 gnupg2-dirmngr                    x86_64 0:2.4.8-4.fc44               copr_base                                                                    633.9 KiB
 gnupg2-gpg-agent                  x86_64 0:2.4.8-4.fc44               copr_base                                                                    686.5 KiB
 gnupg2-gpgconf                    x86_64 0:2.4.8-4.fc44               copr_base                                                                    249.7 KiB
 gnupg2-keyboxd                    x86_64 0:2.4.8-4.fc44               copr_base                                                                    201.2 KiB
 gnupg2-verify                     x86_64 0:2.4.8-4.fc44               copr_base                                                                    360.3 KiB
 gnutls                            x86_64 0:3.8.11-8.fc44              copr_base                                                                      3.7 MiB
 go-srpm-macros                    noarch 0:3.8.0-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  61.9 KiB
 gpgverify                         noarch 0:2.2-3.fc43                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   8.7 KiB
 ima-evm-utils-libs                x86_64 0:1.6.2-7.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  60.7 KiB
 jansson                           x86_64 0:2.14-3.fc44                copr_base                                                                     88.9 KiB
 java-srpm-macros                  noarch 0:1-7.fc43                   https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 870.0   B
 json-c                            x86_64 0:0.18-7.fc44                copr_base                                                                     82.6 KiB
 kernel-srpm-macros                noarch 0:1.0-27.fc43                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.9 KiB
 keyutils-libs                     x86_64 0:1.6.3-6.fc44               copr_base                                                                     54.2 KiB
 krb5-libs                         x86_64 0:1.21.3-10.fc44             https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.3 MiB
 libacl                            x86_64 0:2.3.2-4.fc44               copr_base                                                                     35.8 KiB
 libarchive                        x86_64 0:3.8.4-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 955.3 KiB
 libassuan                         x86_64 0:2.5.7-4.fc44               copr_base                                                                    163.8 KiB
 libatomic                         x86_64 0:16.0.0-0.3.fc44            https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  36.7 KiB
 libattr                           x86_64 0:2.5.2-6.fc43               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  24.4 KiB
 libblkid                          x86_64 0:2.41.3-8.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 262.3 KiB
 libbrotli                         x86_64 0:1.2.0-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 865.4 KiB
 libcap                            x86_64 0:2.77-1.fc44                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 209.1 KiB
 libcap-ng                         x86_64 0:0.8.5-8.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  68.9 KiB
 libcom_err                        x86_64 0:1.47.3-3.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  63.1 KiB
 libcurl                           x86_64 0:8.18.0~rc2-1.fc44          https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 984.7 KiB
 libeconf                          x86_64 0:0.7.9-2.fc44               copr_base                                                                     64.8 KiB
 libevent                          x86_64 0:2.1.12-16.fc44             copr_base                                                                    978.7 KiB
 libfdisk                          x86_64 0:2.41.3-8.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 380.3 KiB
 libffi                            x86_64 0:3.5.2-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  83.8 KiB
 libfsverity                       x86_64 0:1.6-3.fc44                 copr_base                                                                     28.4 KiB
 libgcc                            x86_64 0:16.0.0-0.3.fc44            https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 270.7 KiB
 libgcrypt                         x86_64 0:1.11.2-1.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.6 MiB
 libgomp                           x86_64 0:16.0.0-0.3.fc44            https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 570.9 KiB
 libgpg-error                      x86_64 0:1.58-1.fc44                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 941.6 KiB
 libidn2                           x86_64 0:2.3.8-2.fc44               copr_base                                                                    556.4 KiB
 libksba                           x86_64 0:1.6.7-4.fc44               copr_base                                                                    414.4 KiB
 liblastlog2                       x86_64 0:2.41.3-8.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  33.6 KiB
 libmount                          x86_64 0:2.41.3-8.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 372.6 KiB
 libnghttp2                        x86_64 0:1.68.0-2.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 162.2 KiB
 libnghttp3                        x86_64 0:1.14.0-1.fc44              fedora                                                                       155.2 KiB
 libpkgconf                        x86_64 0:2.3.0-3.fc43               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  78.1 KiB
 libpsl                            x86_64 0:0.21.5-6.fc44              copr_base                                                                     76.3 KiB
 libselinux                        x86_64 0:3.9-5.fc44                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 193.1 KiB
 libselinux-utils                  x86_64 0:3.9-5.fc44                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 309.0 KiB
 libsemanage                       x86_64 0:3.9-4.fc44                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 308.5 KiB
 libsepol                          x86_64 0:3.9-2.fc44                 copr_base                                                                    861.8 KiB
 libsmartcols                      x86_64 0:2.41.3-8.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 180.3 KiB
 libssh                            x86_64 0:0.11.3-1.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 567.1 KiB
 libssh-config                     noarch 0:0.11.3-1.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 277.0   B
 libstdc++                         x86_64 0:16.0.0-0.3.fc44            https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.9 MiB
 libtasn1                          x86_64 0:4.20.0-2.fc44              copr_base                                                                    176.2 KiB
 libtool-ltdl                      x86_64 0:2.5.4-9.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  70.0 KiB
 libunistring                      x86_64 0:1.1-10.fc44                copr_base                                                                      1.7 MiB
 libusb1                           x86_64 0:1.0.29-4.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 171.3 KiB
 libuuid                           x86_64 0:2.41.3-8.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  37.2 KiB
 libverto                          x86_64 0:0.3.2-11.fc43              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  25.4 KiB
 libxcrypt                         x86_64 0:4.5.2-2.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 285.3 KiB
 libxml2                           x86_64 0:2.12.10-5.fc44             https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.7 MiB
 libzstd                           x86_64 0:1.5.7-3.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 940.3 KiB
 linkdupes                         x86_64 0:0.7.2-2.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 838.7 KiB
 lua-libs                          x86_64 0:5.4.8-4.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 281.9 KiB
 lua-srpm-macros                   noarch 0:1-16.fc43                  https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.3 KiB
 lz4-libs                          x86_64 0:1.10.0-3.fc44              copr_base                                                                    157.3 KiB
 mpfr                              x86_64 0:4.2.2-2.fc43               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 832.8 KiB
 ncurses-base                      noarch 0:6.5-8.20250614.fc44        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 328.1 KiB
 ncurses-libs                      x86_64 0:6.5-8.20250614.fc44        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 946.4 KiB
 nettle                            x86_64 0:3.10.1-2.fc43              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 790.6 KiB
 ngtcp2                            x86_64 0:1.18.0-1.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 314.3 KiB
 ngtcp2-crypto-ossl                x86_64 0:1.18.0-1.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  51.7 KiB
 npth                              x86_64 0:1.8-3.fc43                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  49.6 KiB
 ocaml-srpm-macros                 noarch 0:11-2.fc43                  https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.9 KiB
 openblas-srpm-macros              noarch 0:2-20.fc43                  https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 112.0   B
 openldap                          x86_64 0:2.6.10-4.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 659.8 KiB
 openssl-libs                      x86_64 1:3.5.4-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   8.9 MiB
 p11-kit                           x86_64 0:0.25.8-1.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.3 MiB
 p11-kit-trust                     x86_64 0:0.25.8-1.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 446.5 KiB
 package-notes-srpm-macros         noarch 0:0.5-14.fc43                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.6 KiB
 pam-libs                          x86_64 0:1.7.1-3.fc43               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 126.8 KiB
 pcre2                             x86_64 0:10.47-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 702.6 KiB
 pcre2-syntax                      noarch 0:10.47-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 281.9 KiB
 perl-srpm-macros                  noarch 0:1-60.fc43                  https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 861.0   B
 pkgconf                           x86_64 0:2.3.0-3.fc43               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  88.5 KiB
 pkgconf-m4                        noarch 0:2.3.0-3.fc43               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  14.4 KiB
 pkgconf-pkg-config                x86_64 0:2.3.0-3.fc43               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 989.0   B
 policycoreutils                   x86_64 0:3.9-5.fc44                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 683.5 KiB
 popt                              x86_64 0:1.19-9.fc43                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 132.8 KiB
 publicsuffix-list-dafsa           noarch 0:20250616-2.fc43            https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  69.1 KiB
 pyproject-srpm-macros             noarch 0:1.18.6-1.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.9 KiB
 python-srpm-macros                noarch 0:3.14-9.fc44                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  51.6 KiB
 qt5-srpm-macros                   noarch 0:5.15.18-1.fc44             https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 500.0   B
 qt6-srpm-macros                   noarch 0:6.10.1-1.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 464.0   B
 readline                          x86_64 0:8.3-2.fc43                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 511.7 KiB
 rpm                               x86_64 0:6.0.1-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   3.1 MiB
 rpm-build-libs                    x86_64 0:6.0.1-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 264.4 KiB
 rpm-libs                          x86_64 0:6.0.1-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 933.8 KiB
 rpm-plugin-selinux                x86_64 0:6.0.1-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  12.0 KiB
 rpm-sequoia                       x86_64 0:1.10.0-1.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.5 MiB
 rpm-sign-libs                     x86_64 0:6.0.1-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  39.7 KiB
 rust-srpm-macros                  noarch 0:28.4-1.fc44                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   5.5 KiB
 selinux-policy                    noarch 0:42.19-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  32.0 KiB
 selinux-policy-targeted           noarch 0:42.19-1.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  18.7 MiB
 setup                             noarch 0:2.15.0-27.fc44             https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 724.9 KiB
 sqlite-libs                       x86_64 0:3.51.0-1.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.5 MiB
 systemd-libs                      x86_64 0:259-1.fc44                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.3 MiB
 systemd-standalone-sysusers       x86_64 0:259-1.fc44                 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 293.5 KiB
 tpm2-tss                          x86_64 0:4.1.3-8.fc43               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.6 MiB
 tree-sitter-srpm-macros           noarch 0:0.4.2-1.fc43               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   8.3 KiB
 util-linux-core                   x86_64 0:2.41.3-8.fc44              https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.5 MiB
 xxhash-libs                       x86_64 0:0.8.3-3.fc43               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  90.2 KiB
 xz-libs                           x86_64 1:5.8.1-4.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 217.8 KiB
 zig-srpm-macros                   noarch 0:1-5.fc43                   https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.1 KiB
 zip                               x86_64 0:3.0-44.fc43                https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 694.5 KiB
 zlib-ng-compat                    x86_64 0:2.3.2-2.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 161.5 KiB
 zstd                              x86_64 0:1.5.7-3.fc44               https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 506.2 KiB
Installing groups:
 Buildsystem building group                                                                                                                                  

Transaction Summary:
 Installing:       183 packages

Total size of inbound packages is 67 MiB. Need to download 0 B.
After this operation, 220 MiB extra will be used (install 220 MiB, remove 0 B).
[  1/183] tar-2:1.35-6.fc43.x86_64      100% |   0.0   B/s |   0.0   B |  00m00s
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[ 12/183] sed-0:4.9-6.fc44.x86_64       100% |   0.0   B/s |   0.0   B |  00m00s
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[ 15/183] diffutils-0:3.12-3.fc44.x86_6 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 17/183] findutils-1:4.10.0-6.fc44.x86 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 18/183] gawk-0:5.3.2-2.fc44.x86_64    100% |   0.0   B/s |   0.0   B |  00m00s
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[ 25/183] glibc-gconv-extra-0:2.42.9000 100% |   0.0   B/s |   0.0   B |  00m00s
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--------------------------------------------------------------------------------
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Running transaction
Importing OpenPGP key 0x6D9F90A6:
 UserID     : "Fedora (44) <fedora-44-primary@fedoraproject.org>"
 Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary
The key was successfully imported.
Importing OpenPGP key 0x6D9F90A6:
 UserID     : "Fedora (44) <fedora-44-primary@fedoraproject.org>"
 Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary
The key was successfully imported.
Importing OpenPGP key 0x31645531:
 UserID     : "Fedora (43) <fedora-43-primary@fedoraproject.org>"
 Fingerprint: C6E7F081CF80E13146676E88829B606631645531
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary
The key was successfully imported.
Importing OpenPGP key 0xF577861E:
 UserID     : "Fedora (45) <fedora-45-primary@fedoraproject.org>"
 Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary
The key was successfully imported.
[  1/185] Verify package files          100% | 660.0   B/s | 183.0   B |  00m00s
>>> Running %pretrans scriptlet: filesystem-0:3.18-51.fc44.x86_64
>>> Finished %pretrans scriptlet: filesystem-0:3.18-51.fc44.x86_64
>>> [RPM] /var/lib/mock/fedora-rawhide-x86_64-1767054237.482716/root/var/cache/dnf/copr_base-a2b79860a4d039f2/packages/bzip2-1.0.8-21.fc44.x86_64.rpm: Header OpenPGP V4 RSA/SHA256 signature, key ID 52ac7d71d4a9769d: NOKEY
[  2/185] Prepare transaction           100% |   3.4 KiB/s | 183.0   B |  00m00s
[  3/185] Installing libgcc-0:16.0.0-0. 100% | 266.0 MiB/s | 272.4 KiB |  00m00s
[  4/185] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
[  5/185] Installing publicsuffix-list- 100% |   0.0   B/s |  69.8 KiB |  00m00s
[  6/185] Installing fedora-release-ide 100% |   0.0   B/s | 920.0   B |  00m00s
[  7/185] Installing fedora-repos-rawhi 100% |   0.0   B/s |   2.4 KiB |  00m00s
[  8/185] Installing fedora-gpg-keys-0: 100% |  43.7 MiB/s | 179.0 KiB |  00m00s
[  9/185] Installing fedora-repos-0:44- 100% |   0.0   B/s |   5.7 KiB |  00m00s
[ 10/185] Installing fedora-release-com 100% |  24.3 MiB/s |  24.9 KiB |  00m00s
[ 11/185] Installing fedora-release-0:4 100% |  17.3 KiB/s | 124.0   B |  00m00s
>>> Running sysusers scriptlet: setup-0:2.15.0-27.fc44.noarch
>>> Finished sysusers scriptlet: setup-0:2.15.0-27.fc44.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.
>>> 
[ 12/185] Installing setup-0:2.15.0-27. 100% |  51.0 MiB/s | 730.6 KiB |  00m00s
>>> [RPM] /etc/hosts created as /etc/hosts.rpmnew
[ 13/185] Installing filesystem-0:3.18- 100% |   2.8 MiB/s | 212.8 KiB |  00m00s
[ 14/185] Installing gnulib-l10n-0:2024 100% | 215.5 MiB/s | 661.9 KiB |  00m00s
[ 15/185] Installing coreutils-common-0 100% | 387.2 MiB/s |  11.2 MiB |  00m00s
[ 16/185] Installing ncurses-base-0:6.5 100% |  86.3 MiB/s | 353.5 KiB |  00m00s
[ 17/185] Installing bash-0:5.3.0-2.fc4 100% | 282.5 MiB/s |   8.5 MiB |  00m00s
[ 18/185] Installing glibc-common-0:2.4 100% |  64.0 MiB/s |   1.0 MiB |  00m00s
[ 19/185] Installing glibc-gconv-extra- 100% | 280.3 MiB/s |   7.3 MiB |  00m00s
[ 20/185] Installing glibc-0:2.42.9000- 100% | 190.3 MiB/s |   6.8 MiB |  00m00s
[ 21/185] Installing ncurses-libs-0:6.5 100% | 232.7 MiB/s | 953.0 KiB |  00m00s
[ 22/185] Installing glibc-minimal-lang 100% |   0.0   B/s | 124.0   B |  00m00s
[ 23/185] Installing zlib-ng-compat-0:2 100% | 158.6 MiB/s | 162.4 KiB |  00m00s
[ 24/185] Installing bzip2-libs-0:1.0.8 100% |  79.7 MiB/s |  81.6 KiB |  00m00s
[ 25/185] Installing libgpg-error-0:1.5 100% |  66.1 MiB/s | 947.5 KiB |  00m00s
[ 26/185] Installing libassuan-0:2.5.7- 100% | 161.8 MiB/s | 165.7 KiB |  00m00s
[ 27/185] Installing libgcrypt-0:1.11.2 100% | 394.0 MiB/s |   1.6 MiB |  00m00s
[ 28/185] Installing readline-0:8.3-2.f 100% | 250.9 MiB/s | 513.9 KiB |  00m00s
[ 29/185] Installing gmp-1:6.3.0-4.fc44 100% | 399.2 MiB/s | 817.5 KiB |  00m00s
[ 30/185] Installing xz-libs-1:5.8.1-4. 100% | 213.8 MiB/s | 218.9 KiB |  00m00s
[ 31/185] Installing libuuid-0:2.41.3-8 100% |   0.0   B/s |  38.2 KiB |  00m00s
[ 32/185] Installing popt-0:1.19-9.fc43 100% |  68.1 MiB/s | 139.4 KiB |  00m00s
[ 33/185] Installing libzstd-0:1.5.7-3. 100% | 306.5 MiB/s | 941.6 KiB |  00m00s
[ 34/185] Installing elfutils-libelf-0: 100% | 373.7 MiB/s |   1.1 MiB |  00m00s
[ 35/185] Installing npth-0:1.8-3.fc43. 100% |   0.0   B/s |  50.7 KiB |  00m00s
[ 36/185] Installing libblkid-0:2.41.3- 100% | 257.2 MiB/s | 263.4 KiB |  00m00s
[ 37/185] Installing systemd-libs-0:259 100% | 390.0 MiB/s |   2.3 MiB |  00m00s
[ 38/185] Installing libxcrypt-0:4.5.2- 100% | 281.3 MiB/s | 288.0 KiB |  00m00s
[ 39/185] Installing libsepol-0:3.9-2.f 100% | 421.3 MiB/s | 862.8 KiB |  00m00s
[ 40/185] Installing sqlite-libs-0:3.51 100% | 383.0 MiB/s |   1.5 MiB |  00m00s
[ 41/185] Installing gnupg2-gpgconf-0:2 100% |  20.5 MiB/s | 251.8 KiB |  00m00s
[ 42/185] Installing libattr-0:2.5.2-6. 100% |   0.0   B/s |  25.4 KiB |  00m00s
[ 43/185] Installing libacl-0:2.3.2-4.f 100% |   0.0   B/s |  36.6 KiB |  00m00s
[ 44/185] Installing libtasn1-0:4.20.0- 100% | 173.8 MiB/s | 178.0 KiB |  00m00s
[ 45/185] Installing libunistring-0:1.1 100% | 346.9 MiB/s |   1.7 MiB |  00m00s
[ 46/185] Installing libidn2-0:2.3.8-2. 100% |  61.0 MiB/s | 562.6 KiB |  00m00s
[ 47/185] Installing crypto-policies-0: 100% |  38.5 MiB/s | 157.7 KiB |  00m00s
[ 48/185] Installing gnupg2-verify-0:2. 100% |  27.2 MiB/s | 361.7 KiB |  00m00s
[ 49/185] Installing dwz-0:0.16-2.fc44. 100% |  23.8 MiB/s | 292.3 KiB |  00m00s
[ 50/185] Installing mpfr-0:4.2.2-2.fc4 100% | 271.6 MiB/s | 834.4 KiB |  00m00s
[ 51/185] Installing gawk-0:5.3.2-2.fc4 100% | 108.1 MiB/s |   1.8 MiB |  00m00s
[ 52/185] Installing libksba-0:1.6.7-4. 100% | 203.6 MiB/s | 416.9 KiB |  00m00s
[ 53/185] Installing unzip-0:6.0-68.fc4 100% |  32.1 MiB/s | 393.8 KiB |  00m00s
[ 54/185] Installing file-libs-0:5.46-8 100% | 658.7 MiB/s |  11.9 MiB |  00m00s
[ 55/185] Installing file-0:5.46-8.fc44 100% |   8.3 MiB/s | 101.7 KiB |  00m00s
[ 56/185] Installing diffutils-0:3.12-3 100% |  98.3 MiB/s |   1.6 MiB |  00m00s
[ 57/185] Installing libcap-ng-0:0.8.5- 100% |  69.2 MiB/s |  70.8 KiB |  00m00s
[ 58/185] Installing audit-libs-0:4.1.2 100% | 186.3 MiB/s | 381.5 KiB |  00m00s
[ 59/185] Installing libsmartcols-0:2.4 100% | 177.1 MiB/s | 181.4 KiB |  00m00s
[ 60/185] Installing libeconf-0:0.7.9-2 100% |  64.9 MiB/s |  66.4 KiB |  00m00s
[ 61/185] Installing pam-libs-0:1.7.1-3 100% | 126.0 MiB/s | 129.0 KiB |  00m00s
[ 62/185] Installing libcap-0:2.77-1.fc 100% |  17.4 MiB/s | 214.3 KiB |  00m00s
[ 63/185] Installing alternatives-0:1.3 100% |   5.7 MiB/s |  63.8 KiB |  00m00s
[ 64/185] Installing lua-libs-0:5.4.8-4 100% | 276.7 MiB/s | 283.3 KiB |  00m00s
[ 65/185] Installing json-c-0:0.18-7.fc 100% |  81.9 MiB/s |  83.9 KiB |  00m00s
[ 66/185] Installing libffi-0:3.5.2-1.f 100% |  83.2 MiB/s |  85.2 KiB |  00m00s
[ 67/185] Installing p11-kit-0:0.25.8-1 100% | 120.5 MiB/s |   2.3 MiB |  00m00s
[ 68/185] Installing p11-kit-trust-0:0. 100% |  21.9 MiB/s | 448.3 KiB |  00m00s
[ 69/185] Installing ngtcp2-0:1.18.0-1. 100% | 308.4 MiB/s | 315.8 KiB |  00m00s
[ 70/185] Installing zip-0:3.0-44.fc43. 100% |  48.7 MiB/s | 698.4 KiB |  00m00s
[ 71/185] Installing gnupg2-keyboxd-0:2 100% |  33.0 MiB/s | 202.5 KiB |  00m00s
[ 72/185] Installing libpsl-0:0.21.5-6. 100% |  75.6 MiB/s |  77.4 KiB |  00m00s
[ 73/185] Installing liblastlog2-0:2.41 100% |   7.0 MiB/s |  35.8 KiB |  00m00s
[ 74/185] Installing systemd-standalone 100% |  22.1 MiB/s | 294.2 KiB |  00m00s
[ 75/185] Installing libusb1-0:1.0.29-4 100% | 168.9 MiB/s | 172.9 KiB |  00m00s
[ 76/185] Installing libfdisk-0:2.41.3- 100% | 372.4 MiB/s | 381.3 KiB |  00m00s
[ 77/185] Installing libxml2-0:2.12.10- 100% | 106.5 MiB/s |   1.7 MiB |  00m00s
[ 78/185] Installing nettle-0:3.10.1-2. 100% | 258.4 MiB/s | 793.7 KiB |  00m00s
[ 79/185] Installing gnutls-0:3.8.11-8. 100% | 373.4 MiB/s |   3.7 MiB |  00m00s
[ 80/185] Installing bzip2-0:1.0.8-21.f 100% |   8.1 MiB/s |  99.5 KiB |  00m00s
[ 81/185] Installing add-determinism-0: 100% | 135.6 MiB/s |   2.3 MiB |  00m00s
[ 82/185] Installing cpio-0:2.15-6.fc44 100% |  73.6 MiB/s |   1.1 MiB |  00m00s
[ 83/185] Installing libpkgconf-0:2.3.0 100% |   0.0   B/s |  79.2 KiB |  00m00s
[ 84/185] Installing pkgconf-0:2.3.0-3. 100% |   7.4 MiB/s |  91.0 KiB |  00m00s
[ 85/185] Installing ed-0:1.22.3-1.fc44 100% |  13.4 MiB/s | 151.2 KiB |  00m00s
[ 86/185] Installing patch-0:2.8-3.fc44 100% |  18.6 MiB/s | 228.2 KiB |  00m00s
[ 87/185] Installing libatomic-0:16.0.0 100% |   0.0   B/s |  37.5 KiB |  00m00s
[ 88/185] Installing libstdc++-0:16.0.0 100% | 364.8 MiB/s |   2.9 MiB |  00m00s
[ 89/185] Installing zstd-0:1.5.7-3.fc4 100% |  38.3 MiB/s | 509.8 KiB |  00m00s
[ 90/185] Installing lz4-libs-0:1.10.0- 100% | 154.6 MiB/s | 158.4 KiB |  00m00s
[ 91/185] Installing jansson-0:2.14-3.f 100% |  88.2 MiB/s |  90.3 KiB |  00m00s
[ 92/185] Installing libgomp-0:16.0.0-0 100% | 279.4 MiB/s | 572.3 KiB |  00m00s
[ 93/185] Installing libtool-ltdl-0:2.5 100% |  69.5 MiB/s |  71.1 KiB |  00m00s
[ 94/185] Installing gdbm-libs-1:1.23-1 100% | 128.1 MiB/s | 131.2 KiB |  00m00s
[ 95/185] Installing cyrus-sasl-lib-0:2 100% | 135.3 MiB/s |   2.3 MiB |  00m00s
[ 96/185] Installing xxhash-libs-0:0.8. 100% |  89.4 MiB/s |  91.6 KiB |  00m00s
[ 97/185] Installing libbrotli-0:1.2.0- 100% | 282.4 MiB/s | 867.7 KiB |  00m00s
[ 98/185] Installing libnghttp2-0:1.68. 100% | 159.5 MiB/s | 163.4 KiB |  00m00s
[ 99/185] Installing libnghttp3-0:1.14. 100% | 152.9 MiB/s | 156.6 KiB |  00m00s
[100/185] Installing keyutils-libs-0:1. 100% |  54.3 MiB/s |  55.6 KiB |  00m00s
[101/185] Installing libcom_err-0:1.47. 100% |   0.0   B/s |  64.2 KiB |  00m00s
[102/185] Installing libverto-0:0.3.2-1 100% |  26.6 MiB/s |  27.2 KiB |  00m00s
[103/185] Installing filesystem-srpm-ma 100% |   0.0   B/s |  38.9 KiB |  00m00s
[104/185] Installing elfutils-default-y 100% | 408.6 KiB/s |   2.0 KiB |  00m00s
[105/185] Installing elfutils-libs-0:0. 100% | 224.4 MiB/s | 689.3 KiB |  00m00s
[106/185] Installing pcre2-syntax-0:10. 100% | 277.7 MiB/s | 284.3 KiB |  00m00s
[107/185] Installing pcre2-0:10.47-1.fc 100% | 343.8 MiB/s | 704.1 KiB |  00m00s
[108/185] Installing libselinux-0:3.9-5 100% | 189.8 MiB/s | 194.4 KiB |  00m00s
[109/185] Installing grep-0:3.12-2.fc44 100% |  59.0 MiB/s |   1.0 MiB |  00m00s
[110/185] Installing sed-0:4.9-6.fc44.x 100% |  56.3 MiB/s | 865.5 KiB |  00m00s
[111/185] Installing findutils-1:4.10.0 100% | 110.0 MiB/s |   1.9 MiB |  00m00s
[112/185] Installing xz-1:5.8.1-4.fc44. 100% |  78.3 MiB/s |   1.3 MiB |  00m00s
[113/185] Installing libmount-0:2.41.3- 100% | 364.8 MiB/s | 373.6 KiB |  00m00s
[114/185] Installing libsemanage-0:3.9- 100% | 151.5 MiB/s | 310.2 KiB |  00m00s
[115/185] Installing util-linux-core-0: 100% |  86.8 MiB/s |   1.5 MiB |  00m00s
[116/185] Installing openssl-libs-1:3.5 100% | 405.0 MiB/s |   8.9 MiB |  00m00s
[117/185] Installing coreutils-0:9.9-1. 100% | 166.3 MiB/s |   5.5 MiB |  00m00s
[118/185] Installing ca-certificates-0: 100% |   2.1 MiB/s |   2.5 MiB |  00m01s
[119/185] Installing libarchive-0:3.8.4 100% | 233.7 MiB/s | 957.2 KiB |  00m00s
[120/185] Installing krb5-libs-0:1.21.3 100% | 153.3 MiB/s |   2.3 MiB |  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.
>>> 
[121/185] Installing tpm2-tss-0:4.1.3-8 100% | 262.0 MiB/s |   1.6 MiB |  00m00s
[122/185] Installing gnupg2-gpg-agent-0 100% |  33.7 MiB/s | 690.5 KiB |  00m00s
[123/185] Installing ima-evm-utils-libs 100% |  60.5 MiB/s |  62.0 KiB |  00m00s
[124/185] Installing libssh-0:0.11.3-1. 100% | 185.3 MiB/s | 569.2 KiB |  00m00s
[125/185] Installing util-linux-0:2.41. 100% | 108.0 MiB/s |   3.6 MiB |  00m00s
[126/185] Installing gzip-0:1.14-1.fc44 100% |  28.1 MiB/s | 403.3 KiB |  00m00s
[127/185] Installing rpm-sequoia-0:1.10 100% | 352.3 MiB/s |   2.5 MiB |  00m00s
[128/185] Installing rpm-libs-0:6.0.1-1 100% | 304.5 MiB/s | 935.3 KiB |  00m00s
[129/185] Installing libfsverity-0:1.6- 100% |   0.0   B/s |  29.4 KiB |  00m00s
[130/185] Installing libevent-0:2.1.12- 100% | 319.8 MiB/s | 982.4 KiB |  00m00s
[131/185] Installing openldap-0:2.6.10- 100% | 216.0 MiB/s | 663.6 KiB |  00m00s
[132/185] Installing gnupg2-dirmngr-0:2 100% |  34.5 MiB/s | 636.6 KiB |  00m00s
[133/185] Installing gnupg2-0:2.4.8-4.f 100% | 223.8 MiB/s |   6.5 MiB |  00m00s
[134/185] Installing rpm-sign-libs-0:6. 100% |  39.6 MiB/s |  40.6 KiB |  00m00s
[135/185] Installing rpm-build-libs-0:6 100% | 259.0 MiB/s | 265.2 KiB |  00m00s
[136/185] Installing gpgverify-0:2.2-3. 100% |   0.0   B/s |   9.4 KiB |  00m00s
[137/185] Installing ngtcp2-crypto-ossl 100% |   0.0   B/s |  52.6 KiB |  00m00s
[138/185] Installing libcurl-0:8.18.0~r 100% | 320.9 MiB/s | 985.8 KiB |  00m00s
[139/185] Installing elfutils-debuginfo 100% |   7.0 MiB/s |  86.3 KiB |  00m00s
[140/185] Installing binutils-0:2.45.50 100% | 338.9 MiB/s |  27.4 MiB |  00m00s
[141/185] Installing elfutils-0:0.194-2 100% | 154.2 MiB/s |   2.9 MiB |  00m00s
[142/185] Installing gdb-minimal-0:16.3 100% | 294.6 MiB/s |  13.3 MiB |  00m00s
[143/185] Installing debugedit-0:5.2-3. 100% |  16.3 MiB/s | 217.3 KiB |  00m00s
[144/185] Installing curl-0:8.18.0~rc2- 100% |  22.0 MiB/s | 474.1 KiB |  00m00s
[145/185] Installing rpm-0:6.0.1-1.fc44 100% |  82.3 MiB/s |   2.6 MiB |  00m00s
[146/185] Installing cmake-srpm-macros- 100% |   0.0   B/s | 804.0   B |  00m00s
[147/185] Installing efi-srpm-macros-0: 100% |   0.0   B/s |  41.2 KiB |  00m00s
[148/185] Installing java-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[149/185] Installing lua-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[150/185] Installing tree-sitter-srpm-m 100% |   0.0   B/s |   9.3 KiB |  00m00s
[151/185] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.7 KiB |  00m00s
[152/185] Installing tar-2:1.35-6.fc43. 100% | 147.9 MiB/s |   3.0 MiB |  00m00s
[153/185] Installing linkdupes-0:0.7.2- 100% |  58.6 MiB/s | 840.1 KiB |  00m00s
[154/185] Installing libselinux-utils-0 100% |  22.6 MiB/s | 323.4 KiB |  00m00s
[155/185] Installing policycoreutils-0: 100% |  29.0 MiB/s | 711.8 KiB |  00m00s
[156/185] Installing selinux-policy-0:4 100% |   1.9 MiB/s |  33.6 KiB |  00m00s
[157/185] Installing selinux-policy-tar 100% | 198.8 MiB/s |  14.9 MiB |  00m00s
[158/185] Installing build-reproducibil 100% |   0.0   B/s |   1.5 KiB |  00m00s
[159/185] Installing pkgconf-m4-0:2.3.0 100% |   0.0   B/s |  14.8 KiB |  00m00s
[160/185] Installing pkgconf-pkg-config 100% | 136.4 KiB/s |   1.8 KiB |  00m00s
[161/185] Installing rust-srpm-macros-0 100% |   0.0   B/s |   6.4 KiB |  00m00s
[162/185] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 740.0   B |  00m00s
[163/185] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 776.0   B |  00m00s
[164/185] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[165/185] Installing package-notes-srpm 100% |   0.0   B/s |   2.0 KiB |  00m00s
[166/185] Installing openblas-srpm-macr 100% |   0.0   B/s | 392.0   B |  00m00s
[167/185] Installing ocaml-srpm-macros- 100% |   0.0   B/s |   2.1 KiB |  00m00s
[168/185] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[169/185] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[170/185] Installing ghc-srpm-macros-0: 100% |   0.0   B/s |   1.0 KiB |  00m00s
[171/185] Installing gap-srpm-macros-0: 100% |   0.0   B/s |   2.7 KiB |  00m00s
[172/185] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[173/185] Installing ansible-srpm-macro 100% |   0.0   B/s |  36.2 KiB |  00m00s
[174/185] Installing rpm-build-0:6.0.1- 100% |  20.7 MiB/s | 296.6 KiB |  00m00s
[175/185] Installing pyproject-srpm-mac 100% |   0.0   B/s |   2.5 KiB |  00m00s
[176/185] Installing redhat-rpm-config- 100% |  92.7 MiB/s | 189.9 KiB |  00m00s
[177/185] Installing forge-srpm-macros- 100% |   0.0   B/s |  40.3 KiB |  00m00s
[178/185] Installing fonts-srpm-macros- 100% |   0.0   B/s |  57.0 KiB |  00m00s
[179/185] Installing go-srpm-macros-0:3 100% |   0.0   B/s |  63.0 KiB |  00m00s
[180/185] Installing R-srpm-macros-0:1. 100% |   1.0 MiB/s |   4.0 KiB |  00m00s
[181/185] Installing python-srpm-macros 100% |   0.0   B/s |  52.9 KiB |  00m00s
[182/185] Installing rpm-plugin-selinux 100% |   0.0   B/s |  13.0 KiB |  00m00s
[183/185] Installing which-0:2.23-3.fc4 100% |   6.4 MiB/s |  85.7 KiB |  00m00s
[184/185] Installing shadow-utils-2:4.1 100% | 141.9 MiB/s |   4.0 MiB |  00m00s
[185/185] Installing info-0:7.2-7.fc44. 100% |  57.2 KiB/s | 358.3 KiB |  00m06s
Warning: skipped OpenPGP checks for 178 packages from repositories: copr_base, https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch
Complete!
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: R-srpm-macros-1.3.0-1.fc44.noarch
add-determinism-0.7.2-2.fc44.x86_64
alternatives-1.33-3.fc44.x86_64
ansible-srpm-macros-1-18.1.fc43.noarch
audit-libs-4.1.2-2.fc44.x86_64
bash-5.3.0-2.fc44.x86_64
binutils-2.45.50-12.fc44.x86_64
build-reproducibility-srpm-macros-0.7.2-2.fc44.noarch
bzip2-1.0.8-21.fc44.x86_64
bzip2-libs-1.0.8-21.fc44.x86_64
ca-certificates-2025.2.80_v9.0.304-2.fc44.noarch
cmake-srpm-macros-3.31.10-3.fc44.noarch
coreutils-9.9-1.fc44.x86_64
coreutils-common-9.9-1.fc44.x86_64
cpio-2.15-6.fc44.x86_64
crypto-policies-20251128-1.git19878fe.fc44.noarch
curl-8.18.0~rc2-1.fc44.x86_64
cyrus-sasl-lib-2.1.28-33.fc44.x86_64
debugedit-5.2-3.fc44.x86_64
diffutils-3.12-3.fc44.x86_64
dwz-0.16-2.fc44.x86_64
ed-1.22.3-1.fc44.x86_64
efi-srpm-macros-6-5.fc44.noarch
elfutils-0.194-2.fc44.x86_64
elfutils-debuginfod-client-0.194-2.fc44.x86_64
elfutils-default-yama-scope-0.194-2.fc44.noarch
elfutils-libelf-0.194-2.fc44.x86_64
elfutils-libs-0.194-2.fc44.x86_64
fedora-gpg-keys-44-0.1.noarch
fedora-release-44-0.10.noarch
fedora-release-common-44-0.10.noarch
fedora-release-identity-basic-44-0.10.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-3.18-51.fc44.x86_64
filesystem-srpm-macros-3.18-51.fc44.noarch
findutils-4.10.0-6.fc44.x86_64
fonts-srpm-macros-5.0.0-1.fc44.noarch
forge-srpm-macros-0.4.0-3.fc43.noarch
fpc-srpm-macros-1.3-15.fc43.noarch
gap-srpm-macros-2-1.fc44.noarch
gawk-5.3.2-2.fc44.x86_64
gdb-minimal-16.3-6.fc44.x86_64
gdbm-libs-1.23-10.fc44.x86_64
ghc-srpm-macros-1.9.2-3.fc43.noarch
glibc-2.42.9000-17.fc44.x86_64
glibc-common-2.42.9000-17.fc44.x86_64
glibc-gconv-extra-2.42.9000-17.fc44.x86_64
glibc-minimal-langpack-2.42.9000-17.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-3.8.11-8.fc44.x86_64
go-srpm-macros-3.8.0-1.fc44.noarch
gpg-pubkey-36f612dcf27f7d1a48a835e4dbfcf71c6d9f90a6-6786af3b
gpg-pubkey-4f50a6114cd5c6976a7f1179655a4b02f577861e-6888bc98
gpg-pubkey-c6e7f081cf80e13146676e88829b606631645531-66b6dccf
gpgverify-2.2-3.fc43.noarch
grep-3.12-2.fc44.x86_64
gzip-1.14-1.fc44.x86_64
ima-evm-utils-libs-1.6.2-7.fc44.x86_64
info-7.2-7.fc44.x86_64
jansson-2.14-3.fc44.x86_64
java-srpm-macros-1-7.fc43.noarch
json-c-0.18-7.fc44.x86_64
kernel-srpm-macros-1.0-27.fc43.noarch
keyutils-libs-1.6.3-6.fc44.x86_64
krb5-libs-1.21.3-10.fc44.x86_64
libacl-2.3.2-4.fc44.x86_64
libarchive-3.8.4-1.fc44.x86_64
libassuan-2.5.7-4.fc44.x86_64
libatomic-16.0.0-0.3.fc44.x86_64
libattr-2.5.2-6.fc43.x86_64
libblkid-2.41.3-8.fc44.x86_64
libbrotli-1.2.0-1.fc44.x86_64
libcap-2.77-1.fc44.x86_64
libcap-ng-0.8.5-8.fc44.x86_64
libcom_err-1.47.3-3.fc44.x86_64
libcurl-8.18.0~rc2-1.fc44.x86_64
libeconf-0.7.9-2.fc44.x86_64
libevent-2.1.12-16.fc44.x86_64
libfdisk-2.41.3-8.fc44.x86_64
libffi-3.5.2-1.fc44.x86_64
libfsverity-1.6-3.fc44.x86_64
libgcc-16.0.0-0.3.fc44.x86_64
libgcrypt-1.11.2-1.fc44.x86_64
libgomp-16.0.0-0.3.fc44.x86_64
libgpg-error-1.58-1.fc44.x86_64
libidn2-2.3.8-2.fc44.x86_64
libksba-1.6.7-4.fc44.x86_64
liblastlog2-2.41.3-8.fc44.x86_64
libmount-2.41.3-8.fc44.x86_64
libnghttp2-1.68.0-2.fc44.x86_64
libnghttp3-1.14.0-1.fc44.x86_64
libpkgconf-2.3.0-3.fc43.x86_64
libpsl-0.21.5-6.fc44.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.fc44.x86_64
libsmartcols-2.41.3-8.fc44.x86_64
libssh-0.11.3-1.fc44.x86_64
libssh-config-0.11.3-1.fc44.noarch
libstdc++-16.0.0-0.3.fc44.x86_64
libtasn1-4.20.0-2.fc44.x86_64
libtool-ltdl-2.5.4-9.fc44.x86_64
libunistring-1.1-10.fc44.x86_64
libusb1-1.0.29-4.fc44.x86_64
libuuid-2.41.3-8.fc44.x86_64
libverto-0.3.2-11.fc43.x86_64
libxcrypt-4.5.2-2.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-5.4.8-4.fc44.x86_64
lua-srpm-macros-1-16.fc43.noarch
lz4-libs-1.10.0-3.fc44.x86_64
mpfr-4.2.2-2.fc43.x86_64
ncurses-base-6.5-8.20250614.fc44.noarch
ncurses-libs-6.5-8.20250614.fc44.x86_64
nettle-3.10.1-2.fc43.x86_64
ngtcp2-1.18.0-1.fc44.x86_64
ngtcp2-crypto-ossl-1.18.0-1.fc44.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-3.5.4-1.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-2.8-3.fc44.x86_64
pcre2-10.47-1.fc44.x86_64
pcre2-syntax-10.47-1.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-1.18.6-1.fc44.noarch
python-srpm-macros-3.14-9.fc44.noarch
qt5-srpm-macros-5.15.18-1.fc44.noarch
qt6-srpm-macros-6.10.1-1.fc44.noarch
readline-8.3-2.fc43.x86_64
redhat-rpm-config-343-19.fc44.noarch
rpm-6.0.1-1.fc44.x86_64
rpm-build-6.0.1-1.fc44.x86_64
rpm-build-libs-6.0.1-1.fc44.x86_64
rpm-libs-6.0.1-1.fc44.x86_64
rpm-plugin-selinux-6.0.1-1.fc44.x86_64
rpm-sequoia-1.10.0-1.fc44.x86_64
rpm-sign-libs-6.0.1-1.fc44.x86_64
rust-srpm-macros-28.4-1.fc44.noarch
sed-4.9-6.fc44.x86_64
selinux-policy-42.19-1.fc44.noarch
selinux-policy-targeted-42.19-1.fc44.noarch
setup-2.15.0-27.fc44.noarch
shadow-utils-4.18.0-7.fc44.x86_64
sqlite-libs-3.51.0-1.fc44.x86_64
systemd-libs-259-1.fc44.x86_64
systemd-standalone-sysusers-259-1.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-2.41.3-8.fc44.x86_64
util-linux-core-2.41.3-8.fc44.x86_64
which-2.23-3.fc43.x86_64
xxhash-libs-0.8.3-3.fc43.x86_64
xz-5.8.1-4.fc44.x86_64
xz-libs-5.8.1-4.fc44.x86_64
zig-srpm-macros-1-5.fc43.noarch
zip-3.0-44.fc43.x86_64
zlib-ng-compat-2.3.2-2.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/mmseq-1.0.11-24.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_64-1767054237.482716/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-3ja8g1tx/mmseq/mmseq.spec) Config(child) 0 minutes 17 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/mmseq-1.0.11-24.fc44.src.rpm)  Config(fedora-rawhide-x86_64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1767054237.482716/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1767054237.482716/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_64-1767054237.482716/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-6.0.1-1.fc44.x86_64
  rpm-sequoia-1.10.0-1.fc44.x86_64
  dnf5-5.3.0.0-3.fc44.x86_64
  dnf5-plugins-5.3.0.0-3.fc44.x86_64
Finish: chroot init
Start: build phase for mmseq-1.0.11-24.fc44.src.rpm
Start: build setup for mmseq-1.0.11-24.fc44.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1753315200
Wrote: /builddir/build/SRPMS/mmseq-1.0.11-24.fc44.src.rpm
Updating and loading repositories:
 Additional repo https_kojipkgs_fedorap 100% |   5.0 KiB/s |   3.5 KiB |  00m01s
 Copr repository                        100% |   2.2 KiB/s |   1.5 KiB |  00m01s
 fedora                                 100% |  30.7 KiB/s |  30.6 KiB |  00m01s
Repositories loaded.
Package                      Arch   Version                Repository                                                                        Size
Installing:
 armadillo-devel             x86_64 0:12.8.1-7.fc44        copr_base                                                                      7.3 MiB
 boost-devel                 x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 143.0 MiB
 flexiblas-devel             x86_64 0:3.5.0-1.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   5.9 MiB
 gcc-c++                     x86_64 0:16.0.0-0.3.fc44      https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  48.3 MiB
 gsl-devel                   x86_64 0:2.8-2.fc44           copr_base                                                                      1.6 MiB
 htslib-devel                x86_64 0:1.15.1-9.fc44        copr_base                                                                    411.1 KiB
 make                        x86_64 1:4.4.1-11.fc44        copr_base                                                                      1.8 MiB
 perl-generators             noarch 0:1.16-8.fc43          https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  21.8 KiB
 zlib-ng-compat-devel        x86_64 0:2.3.2-2.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 107.0 KiB
Installing dependencies:
 SuperLU                     x86_64 0:7.0.1-2.fc44         copr_base                                                                    490.1 KiB
 SuperLU-devel               x86_64 0:7.0.1-2.fc44         copr_base                                                                    104.2 KiB
 annobin-docs                noarch 0:13.04-3.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  99.2 KiB
 annobin-plugin-gcc          x86_64 0:13.04-3.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 695.6 KiB
 armadillo                   x86_64 0:12.8.1-7.fc44        copr_base                                                                     81.9 KiB
 arpack                      x86_64 0:3.9.1-7.fc43         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 641.8 KiB
 arpack-devel                x86_64 0:3.9.1-7.fc43         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  69.1 KiB
 boost                       x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.3 KiB
 boost-atomic                x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  20.9 KiB
 boost-chrono                x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  37.5 KiB
 boost-container             x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  65.4 KiB
 boost-context               x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  12.4 KiB
 boost-contract              x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  99.1 KiB
 boost-coroutine             x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  21.1 KiB
 boost-date-time             x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  12.2 KiB
 boost-fiber                 x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  78.7 KiB
 boost-filesystem            x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 143.6 KiB
 boost-graph                 x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 363.1 KiB
 boost-iostreams             x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  90.6 KiB
 boost-json                  x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 333.1 KiB
 boost-locale                x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 617.7 KiB
 boost-log                   x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.5 MiB
 boost-math                  x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 642.6 KiB
 boost-nowide                x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  20.8 KiB
 boost-numpy3                x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  57.6 KiB
 boost-program-options       x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 280.8 KiB
 boost-python3               x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 258.2 KiB
 boost-random                x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  29.6 KiB
 boost-regex                 x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 291.2 KiB
 boost-serialization         x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 441.6 KiB
 boost-stacktrace            x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  59.8 KiB
 boost-system                x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  12.2 KiB
 boost-test                  x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 647.2 KiB
 boost-thread                x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 132.7 KiB
 boost-timer                 x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  21.0 KiB
 boost-type_erasure          x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  54.1 KiB
 boost-wave                  x86_64 0:1.83.0-17.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 868.3 KiB
 cmake-filesystem            x86_64 0:3.31.10-3.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   0.0   B
 cpp                         x86_64 0:16.0.0-0.3.fc44      https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  43.6 MiB
 expat                       x86_64 0:2.7.3-1.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 301.1 KiB
 flexiblas                   x86_64 0:3.5.0-1.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  38.0 KiB
 flexiblas-netlib            x86_64 0:3.5.0-1.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  16.5 MiB
 flexiblas-netlib64          x86_64 0:3.5.0-1.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  16.7 MiB
 flexiblas-openblas-openmp   x86_64 0:3.5.0-1.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  39.2 KiB
 flexiblas-openblas-openmp64 x86_64 0:3.5.0-1.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  39.2 KiB
 gcc                         x86_64 0:16.0.0-0.3.fc44      https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 126.0 MiB
 gcc-gfortran                x86_64 0:16.0.0-0.3.fc44      https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  46.2 MiB
 gcc-plugin-annobin          x86_64 0:16.0.0-0.3.fc44      https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  57.2 KiB
 glibc-devel                 x86_64 0:2.42.9000-17.fc44    fedora                                                                         2.3 MiB
 groff-base                  x86_64 0:1.23.0-11.fc44       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   3.8 MiB
 gsl                         x86_64 0:2.8-2.fc44           copr_base                                                                      3.5 MiB
 hdf5                        x86_64 0:1.14.6-6.fc44        copr_base                                                                      6.5 MiB
 hdf5-devel                  x86_64 0:1.14.6-6.fc44        copr_base                                                                      3.3 MiB
 htslib                      x86_64 0:1.15.1-9.fc44        copr_base                                                                      1.1 MiB
 kernel-headers              x86_64 0:6.19.0-0.rc2.20.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   6.9 MiB
 libaec                      x86_64 0:1.1.4-4.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  90.1 KiB
 libaec-devel                x86_64 0:1.1.4-4.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  22.4 KiB
 libgfortran                 x86_64 0:16.0.0-0.3.fc44      https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   3.4 MiB
 libicu                      x86_64 0:77.1-1.fc44          copr_base                                                                     36.6 MiB
 libicu-devel                x86_64 0:77.1-1.fc44          copr_base                                                                      5.0 MiB
 libmpc                      x86_64 0:1.3.1-8.fc44         copr_base                                                                    160.4 KiB
 libquadmath                 x86_64 0:16.0.0-0.3.fc44      https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 325.9 KiB
 libquadmath-devel           x86_64 0:16.0.0-0.3.fc44      https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  22.1 KiB
 libstdc++-devel             x86_64 0:16.0.0-0.3.fc44      https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  38.7 MiB
 libxcrypt-devel             x86_64 0:4.5.2-2.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  31.0 KiB
 metis                       x86_64 0:5.1.0.3-11.fc44      copr_base                                                                    987.1 KiB
 mpdecimal                   x86_64 0:4.0.1-2.fc43         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 217.2 KiB
 ncurses                     x86_64 0:6.5-8.20250614.fc44  https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 609.8 KiB
 openblas                    x86_64 0:0.3.29-2.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 111.7 KiB
 openblas-openmp             x86_64 0:0.3.29-2.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  43.7 MiB
 openblas-openmp64           x86_64 0:0.3.29-2.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  43.8 MiB
 perl-AutoLoader             noarch 0:5.74-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  20.6 KiB
 perl-B                      x86_64 0:1.89-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 501.3 KiB
 perl-Carp                   noarch 0:1.54-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  46.6 KiB
 perl-Class-Struct           noarch 0:0.68-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  25.4 KiB
 perl-Data-Dumper            x86_64 0:2.191-521.fc43       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 115.6 KiB
 perl-Digest                 noarch 0:1.20-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  35.3 KiB
 perl-Digest-MD5             x86_64 0:2.59-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  59.7 KiB
 perl-DynaLoader             x86_64 0:1.57-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  32.1 KiB
 perl-Encode                 x86_64 4:3.21-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   4.7 MiB
 perl-Errno                  x86_64 0:1.38-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   8.4 KiB
 perl-Exporter               noarch 0:5.79-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  54.3 KiB
 perl-Fcntl                  x86_64 0:1.20-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  48.8 KiB
 perl-Fedora-VSP             noarch 0:0.001-37.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  39.7 KiB
 perl-File-Basename          noarch 0:2.86-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  14.0 KiB
 perl-File-Path              noarch 0:2.18-521.fc44        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  63.5 KiB
 perl-File-Temp              noarch 1:0.231.200-1.fc44     https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 163.7 KiB
 perl-File-stat              noarch 0:1.14-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  12.5 KiB
 perl-FileHandle             noarch 0:2.05-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   9.4 KiB
 perl-Getopt-Long            noarch 1:2.58-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 144.5 KiB
 perl-Getopt-Std             noarch 0:1.14-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  11.2 KiB
 perl-HTTP-Tiny              noarch 0:0.090-521.fc43       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 154.4 KiB
 perl-IO                     x86_64 0:1.55-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 147.4 KiB
 perl-IO-Socket-IP           noarch 0:0.43-521.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 100.3 KiB
 perl-IO-Socket-SSL          noarch 0:2.095-2.fc43         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 714.5 KiB
 perl-IPC-Open3              noarch 0:1.24-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  27.7 KiB
 perl-MIME-Base32            noarch 0:1.303-24.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  30.7 KiB
 perl-MIME-Base64            x86_64 0:3.16-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  42.0 KiB
 perl-Net-SSLeay             x86_64 0:1.94-11.fc43         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.3 MiB
 perl-POSIX                  x86_64 0:2.23-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 231.4 KiB
 perl-PathTools              x86_64 0:3.94-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 180.0 KiB
 perl-Pod-Escapes            noarch 1:1.07-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  24.9 KiB
 perl-Pod-Perldoc            noarch 0:3.28.01-521.fc43     https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 163.7 KiB
 perl-Pod-Simple             noarch 1:3.47-3.fc43          https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 565.3 KiB
 perl-Pod-Usage              noarch 4:2.05-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  86.3 KiB
 perl-Scalar-List-Utils      x86_64 5:1.70-1.fc43          https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 144.9 KiB
 perl-SelectSaver            noarch 0:1.02-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.2 KiB
 perl-Socket                 x86_64 4:2.040-2.fc43         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 120.3 KiB
 perl-Storable               x86_64 1:3.37-521.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 231.2 KiB
 perl-Symbol                 noarch 0:1.09-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   6.8 KiB
 perl-Term-ANSIColor         noarch 0:5.01-521.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  97.5 KiB
 perl-Term-Cap               noarch 0:1.18-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  29.3 KiB
 perl-Text-ParseWords        noarch 0:3.31-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  13.6 KiB
 perl-Text-Tabs+Wrap         noarch 0:2024.001-520.fc43    https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  22.6 KiB
 perl-Time-Local             noarch 2:1.350-520.fc43       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  69.0 KiB
 perl-URI                    noarch 0:5.34-2.fc44          https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 268.0 KiB
 perl-base                   noarch 0:2.27-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  12.6 KiB
 perl-constant               noarch 0:1.33-521.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  26.2 KiB
 perl-if                     noarch 0:0.61.000-520.fc43    https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   5.8 KiB
 perl-interpreter            x86_64 4:5.42.0-520.fc43      https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 118.6 KiB
 perl-libnet                 noarch 0:3.15-521.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 289.4 KiB
 perl-libs                   x86_64 4:5.42.0-520.fc43      https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  11.5 MiB
 perl-locale                 noarch 0:1.13-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   6.1 KiB
 perl-macros                 noarch 4:5.42.0-520.fc43      https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   5.5 KiB
 perl-mro                    x86_64 0:1.29-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  41.6 KiB
 perl-overload               noarch 0:1.40-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  71.6 KiB
 perl-overloading            noarch 0:0.02-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   4.9 KiB
 perl-parent                 noarch 1:0.244-520.fc43       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  10.3 KiB
 perl-podlators              noarch 1:6.0.2-520.fc43       https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 317.5 KiB
 perl-vars                   noarch 0:1.05-520.fc43        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   3.9 KiB
 python-pip-wheel            noarch 0:25.3-1.fc44          https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.2 MiB
 python3                     x86_64 0:3.14.2-1.fc44        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  28.9 KiB
 python3-libs                x86_64 0:3.14.2-1.fc44        https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  43.1 MiB
 python3-numpy               x86_64 1:2.4.0-1.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch  41.0 MiB
 python3-numpy-f2py          x86_64 1:2.4.0-1.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   2.1 MiB
 tzdata                      noarch 0:2025c-1.fc44         https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch   1.2 MiB

Transaction Summary:
 Installing:       145 packages

Total size of inbound packages is 185 MiB. Need to download 29 MiB.
After this operation, 780 MiB extra will be used (install 780 MiB, remove 0 B).
[  1/145] flexiblas-devel-0:3.5.0-1.fc4 100% |   0.0   B/s |   0.0   B |  00m00s
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[  2/145] gcc-c++-0:16.0.0-0.3.fc44.x86 100% |   0.0   B/s |   0.0   B |  00m00s
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[  4/145] zlib-ng-compat-devel-0:2.3.2- 100% |   0.0   B/s |   0.0   B |  00m00s
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[  8/145] arpack-0:3.9.1-7.fc43.x86_64  100% |   0.0   B/s |   0.0   B |  00m00s
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[  9/145] flexiblas-netlib-0:3.5.0-1.fc 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 10/145] cmake-filesystem-0:3.31.10-3. 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 11/145] perl-File-Basename-0:2.86-520 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 14/145] perl-Exporter-0:5.79-520.fc43 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 16/145] gcc-0:16.0.0-0.3.fc44.x86_64  100% |   0.0   B/s |   0.0   B |  00m00s
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[ 17/145] libmpc-0:1.3.1-8.fc44.x86_64  100% |   0.0   B/s |   0.0   B |  00m00s
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[ 18/145] cpp-0:16.0.0-0.3.fc44.x86_64  100% |   0.0   B/s |   0.0   B |  00m00s
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[ 19/145] glibc-devel-0:2.42.9000-17.fc 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 20/145] flexiblas-0:3.5.0-1.fc44.x86_ 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 21/145] flexiblas-openblas-openmp-0:3 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 22/145] libgfortran-0:16.0.0-0.3.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 23/145] libquadmath-0:16.0.0-0.3.fc44 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 24/145] flexiblas-netlib64-0:3.5.0-1. 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 25/145] libicu-0:77.1-1.fc44.x86_64   100% |   0.0   B/s |   0.0   B |  00m00s
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[ 26/145] libquadmath-devel-0:16.0.0-0. 100% |   0.0   B/s |   0.0   B |  00m00s
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[ 29/145] kernel-headers-0:6.19.0-0.rc2 100% |   0.0   B/s |   0.0   B |  00m00s
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[145/145] Total                         100% |   2.9 MiB/s |  28.8 MiB |  00m10s
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Warning: skipped OpenPGP checks for 144 packages from repositories: copr_base, https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch
Complete!
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1753315200
Wrote: /builddir/build/SRPMS/mmseq-1.0.11-24.fc44.src.rpm
Updating and loading repositories:
 Additional repo https_kojipkgs_fedorap 100% |  85.2 KiB/s |   3.5 KiB |  00m00s
 Copr repository                        100% |  37.5 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% | 263.8 KiB/s |  30.6 KiB |  00m00s
Repositories loaded.
Nothing to do.
Package "armadillo-devel-12.8.1-7.fc44.x86_64" is already installed.
Package "boost-devel-1.83.0-17.fc44.x86_64" is already installed.
Package "flexiblas-devel-3.5.0-1.fc44.x86_64" is already installed.
Package "gcc-c++-16.0.0-0.3.fc44.x86_64" is already installed.
Package "gsl-devel-2.8-2.fc44.x86_64" is already installed.
Package "htslib-devel-1.15.1-9.fc44.x86_64" is already installed.
Package "make-1:4.4.1-11.fc44.x86_64" is already installed.
Package "perl-generators-1.16-8.fc43.noarch" is already installed.
Package "zlib-ng-compat-devel-2.3.2-2.fc44.x86_64" is already installed.

Finish: build setup for mmseq-1.0.11-24.fc44.src.rpm
Start: rpmbuild mmseq-1.0.11-24.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.8yfU4d
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.DJziGv
+ umask 022
+ cd /builddir/build/BUILD/mmseq-1.0.11-build
+ cd /builddir/build/BUILD/mmseq-1.0.11-build
+ rm -rf mmseq-1.0.11
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/1.0.11.zip
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd mmseq-1.0.11
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
Patch #2 (mmseq-zlib.patch):
+ echo 'Patch #2 (mmseq-zlib.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .mmseq-zlib.patch --fuzz=0
patching file src/Makefile
+ rm -f bin/offsetGTF-linux bin/postdiff-linux
+ sed -e s/-lblas/-lflexiblas/g -e s/-llapack/-lflexiblas/g -i src/Makefile
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.aG11Qm
+ umask 022
+ cd /builddir/build/BUILD/mmseq-1.0.11-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 mmseq-1.0.11
+ cd src
+ make -j4 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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'
g++ -O3 -c sokal.cc
g++ -fopenmp -O3 -c uh.cpp 
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -fopenmp -O3 hitsio.cpp hitsio.hpp -c hitsio.cpp
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     -c -o fasta.o fasta.c
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -O3 offsetGTF.cpp -o ../bin/offsetGTF
offsetGTF.cpp: In function ‘int main(int, char**)’:
offsetGTF.cpp:115:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  115 |       while(gff_ind < gff_positions[chrom].size()) {
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
offsetGTF.cpp:117:57: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} [-Wsign-compare]
  117 |               pos + tokens[3].size() - tokens[4].size() >= gff_positions[chrom][gff_ind]) {
offsetGTF.cpp:114:11: warning: unused variable ‘curoff’ [-Wunused-variable]
  114 |       int curoff=offset;
      |           ^~~~~~
offsetGTF.cpp:150:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  150 |       while(gff_ind < gff_positions[prevchrom].size()) {
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
offsetGTF.cpp:163:53: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} [-Wsign-compare]
  163 |           pos + tokens[3].size() - tokens[4].size() >= gff_positions[chrom][gff_ind]) {
offsetGTF.cpp:177:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  177 |     while(gff_ind < gff_positions[chrom].size() && gff_positions[chrom][gff_ind] <= pos) {
      |           ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
offsetGTF.cpp:235:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  235 |     for(int i=5; i < tokens.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~
offsetGTF.cpp:237:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  237 |       if(i < tokens.size()-1) {
      |          ~~^~~~~~~~~~~~~~~~~
offsetGTF.cpp:108:7: warning: unused variable ‘gff_pos’ [-Wunused-variable]
  108 |   int gff_pos= -1;
      |       ^~~~~~~
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -O3 t2g_hits.cpp -o ../bin/t2g_hits
t2g_hits.cpp: In function ‘int main(int, char**)’:
t2g_hits.cpp:90:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   90 |         for(int i=2; i < tokens.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~
t2g_hits.cpp:112:13: warning: ignoring return value of ‘constexpr _FIter std::unique(_FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<__cxx11::basic_string<char>*, vector<__cxx11::basic_string<char> > >]’, declared with attribute ‘nodiscard’ [-Wunused-result]
  112 |       unique(comb.begin(), comb.end());
      |       ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/16/algorithm:63,
                 from t2g_hits.cpp:27:
/usr/include/c++/16/bits/stl_algo.h:872:5: note: declared here
  872 |     unique(_ForwardIterator __first, _ForwardIterator __last)
      |     ^~~~~~
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -fopenmp -O2 bms.cpp bms.hpp -c bms.cpp
hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema0()’:
hitsio.cpp:163:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  163 |         for(int i = 0; i < transcriptName.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema0()’:
hitsio.cpp:184:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  184 |         for(int i = 0; i < currentReadTranscripts.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema1()’:
hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   24 |         if (VAL > numeric_limits<uint32_t>::max()) { \
      |                 ^
hitsio.cpp:191:9: note: in expansion of macro ‘WRITE_UINT’
  191 |         WRITE_UINT(ofs, hitsfileSchema);
      |         ^~~~~~~~~~
hitsio.cpp:193:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  193 |         for(int i = 0; i < transcriptName.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘std::map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
   24 |         if (VAL > numeric_limits<uint32_t>::max()) { \
hitsio.cpp:196:17: note: in expansion of macro ‘WRITE_UINT’
  196 |                 WRITE_UINT(ofs, transcriptTrueLength[transcriptName[i] ])
      |                 ^~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema1()’:
hitsio.cpp:236:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  236 |         for(int i = 0; i < currentReadTranscripts.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileReader::readHeaderSchema1(std::vector<std::__cxx11::basic_string<char> >*, std::map<std::__cxx11::basic_string<char>, double>*, std::map<std::__cxx11::basic_string<char>, int>*, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >*, std::vector<std::vector<std::__cxx11::basic_string<char> > >*)’:
hitsio.cpp:356:16: warning: unused variable ‘nextStrLen’ [-Wunused-variable]
  356 |         size_t nextStrLen;
      |                ^~~~~~~~~~
hitsio.cpp: In member function ‘bool HitsfileReader::readReadMapRecordTranscriptID(std::string&)’:
hitsio.cpp:447:1: warning: control reaches end of non-void function [-Wreturn-type]
  447 | }
      | ^
bms.cpp: In member function ‘arma::Col<int> BMS::m2v(arma::Mat<double>)’:
bms.cpp:36:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   36 |   for(int i=0; i < P.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:37:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   37 |     for(int j=0; j < P.n_rows; j++) {
      |                  ~~^~~~~~~~~~
bms.cpp: In member function ‘std::vector<double> BMS::meanvar(arma::Col<double>)’:
bms.cpp:76:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   76 |   for(int i=0;i < v.n_elem; i++) {
      |               ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::print(bool)’:
bms.cpp:93:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   93 |   for(int feature=0; feature < y->n_rows; feature++) {
      |                      ~~~~~~~~^~~~~~~~~~~
bms.cpp:97:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   97 |       for(int i=0; i < M.n_cols; i++) {
      |                    ~~^~~~~~~~~~
bms.cpp:102:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  102 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::printtune(int)’:
bms.cpp:132:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  132 |   for(int feature=0; feature < y->n_rows; feature++) {
      |                      ~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_alpha()’:
bms.cpp:185:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  185 |     for(int j=0; j < y->n_rows; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_beta()’:
bms.cpp:253:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  253 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:255:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  255 |       for(int b=0; b < M.n_cols; b++) {
      |                    ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_eta()’:
bms.cpp:332:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  332 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:334:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  334 |       for(int c=0; c < P[model].n_cols; c++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_sigmasq()’:
bms.cpp:415:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  415 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_lambda()’:
bms.cpp:504:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  504 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:506:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  506 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_rho()’:
bms.cpp:559:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  559 |     for(int j=0; j < y->n_rows; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::copy_pseudo()’:
bms.cpp:582:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  582 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:585:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  585 |     for(int c=0; c < P[0].n_cols; c++) {
      |                  ~~^~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_alpha(int, int, bool)’:
bms.cpp:603:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  603 |     for(int j=0; j < y->n_cols; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:610:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  610 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_beta(int, int, bool)’:
bms.cpp:631:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  631 |     for(int j=0; j < y->n_cols; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:638:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  638 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  646 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  651 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_eta(int, int, bool)’:
bms.cpp:663:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  663 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:666:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  666 |       for(int i=0; i < y->n_cols; i++) {
      |                    ~~^~~~~~~~~~~
bms.cpp:673:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  673 |       for(int i=0; i < y->n_cols; i++) {
      |                    ~~^~~~~~~~~~~
bms.cpp:681:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  681 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:686:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  686 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_lambda(int, int, bool)’:
bms.cpp:699:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  699 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:704:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  704 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:711:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  711 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_sigmasq(int, int, bool, bool)’:
bms.cpp:729:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  729 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:740:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  740 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:751:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  751 |         for(int i=0; i < y->n_cols; i++) {
      |                      ~~^~~~~~~~~~~
bms.cpp:763:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  763 |         for(int i=0; i < y->n_cols; i++) {
      |                      ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_sigmasq_RW(int, int, bool, bool)’:
bms.cpp:877:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  877 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘double BMS::log_target_posterior(int, int)’:
bms.cpp:931:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  931 |   for(int i=0; i < y->n_cols; i++) {
      |                ~~^~~~~~~~~~~
bms.cpp:940:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  940 |     for(int j=0; j < M.n_cols; j++) {
      |                  ~~^~~~~~~~~~
bms.cpp:947:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  947 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘double BMS::log_target_pseudo(int, int)’:
bms.cpp:968:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  968 |     for(int l=0; l < M.n_cols; l++) {
      |                  ~~^~~~~~~~~~
bms.cpp:974:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  974 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::print_pseudo()’:
bms.cpp:1086:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1086 |     for(int l=0; l < M.n_cols; l++) {
      |                  ~~^~~~~~~~~~
bms.cpp:1089:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1089 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:1100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1100 |   for(int i=0; i < y->n_rows; i++) {
      |                ~~^~~~~~~~~~~
bms.cpp:1103:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1103 |       for(int l=0; l < M.n_cols; l++) {
      |                    ~~^~~~~~~~~~
bms.cpp:1106:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1106 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In constructor ‘BMS::BMS(const arma::Mat<double>*, const arma::Mat<double>&, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<int>, double, double, double, std::string, gsl_rng**, int, bool)’:
bms.cpp:1188:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1188 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:1192:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1192 |         if(C(i,model)+1 > _n.size()) {
      |            ~~~~~~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::initialise_streams(std::string)’:
bms.cpp:1348:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1348 |   for(int i=0; i < M.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:1354:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1354 |   for(int i=0; i < M.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:1360:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1360 |   for(int i=0; i < P[0].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1366:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1366 |   for(int i=0; i < P[1].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1372:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1372 |   for(int i=0; i < P[0].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1378:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1378 |   for(int i=0; i < P[1].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -O3 fasta.o extract_transcripts.cpp -o ../bin/extract_transcripts
g++ -DVERSION=1.0.11 -DARMA_64BIT_WORD -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -fopenmp -O3 uh.o sokal.o mmcollapse.cpp -o ../bin/mmcollapse -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
extract_transcripts.cpp: In function ‘int main(int, char**)’:
extract_transcripts.cpp:122:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  122 |       for(int i=0; i < tokens2.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~
extract_transcripts.cpp:169:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  169 |     for(int i=0; i < tokens.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~
extract_transcripts.cpp:195:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  195 |       for(int i=0; i < it->starts()->size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~
extract_transcripts.cpp:203:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  203 |       while(faline < stitch.size()) {
      |             ~~~~~~~^~~~~~~~~~~~~~~
extract_transcripts.cpp:108:7: warning: unused variable ‘line’ [-Wunused-variable]
  108 |   int line=0;
      |       ^~~~
mmcollapse.cpp: In function ‘void get_unidentifiable_transcripts(std::string, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> >&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> >&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> >&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::map<std::__cxx11::basic_string<char>, bool>&)’:
mmcollapse.cpp:158:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  158 |   for(int i=0; i < tokens.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~
mmcollapse.cpp:213:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  213 |     for(int i=0; i < tokens2.size(); i++) isIdent[tokens2[i]]=1;
      |                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:259:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  259 |   for(int i=0; i < tokens.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~
mmcollapse.cpp:307:7: warning: variable ‘v’ set but not used [-Wunused-but-set-variable=]
  307 |   int v=0;
      |       ^
mmcollapse.cpp: In function ‘void collapse(arma::cube&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<int, std::allocator<int> >)’:
mmcollapse.cpp:400:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  400 |   for(int s=0; s < R.n_slices; s++) {
      |                ~~^~~~~~~~~~~~
mmcollapse.cpp:401:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  401 |     for(int t=0; t < candidates.size(); t++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~
mmcollapse.cpp:402:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  402 |       for(int j=1; j < indexes.size(); j++) {
      |                    ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:414:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  414 |     for(int j=1; j < indexes.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:417:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  417 |       for(int i=0; i < R.n_cols; i++) {
      |                    ~~^~~~~~~~~~
mmcollapse.cpp:426:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  426 |   for(int i=0; i < indexes.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:431:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  431 |   for(int i=1; i < tset.size(); i++) {
      |                ~~^~~~~~~~~~~~~
mmcollapse.cpp:437:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  437 |   for(int i=1; i < indexes.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp: In function ‘std::map<int, int> join_traces(arma::mat&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >)’:
mmcollapse.cpp:445:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  445 |   for(int t=0; t < allnames.size(); t++) tmap[allnames[t]]=t;
      |                ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:452:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  452 |   for(int c=0; c < candidates.size(); c++) {
      |                ~~^~~~~~~~~~~~~~~~~~~
mmcollapse.cpp:456:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  456 |     for(int t=0; t < tokens.size(); t++) {
      |                  ~~^~~~~~~~~~~~~~~
mmcollapse.cpp:464:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  464 |     for(int t=1; t < indexes.size(); t++) {
      |                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:469:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  469 |     for(int t=1; t < indexes.size(); t++) {
      |                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:476:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  476 |   for(int i=0; i < toshed.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~
mmcollapse.cpp: In function ‘void mean_corrs(const arma::cube&, const arma::umat&, arma::mat&, arma::mat&, std::vector<int, std::allocator<int> >, std::vector<int, std::allocator<int> >, double)’:
mmcollapse.cpp:486:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  486 |     for(int v= 0; v < R.n_rows; v++) {
      |                   ~~^~~~~~~~~~
mmcollapse.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘long long unsigned int’} [-Wsign-compare]
  492 |       for(int i=0; i < u.size(); i++) {
      |                    ~~^~~~~~~~~~
mmcollapse.cpp: In function ‘void get_corrs(arma::cube&, arma::mat&, const std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::map<std::__cxx11::basic_string<char>, int>&)’:
mmcollapse.cpp:519:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  519 |   for(int s=0; s < basenames.size(); s++) {
      |                ~~^~~~~~~~~~~~~~~~~~
mmcollapse.cpp:543:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  543 |         for(int t=0; t < tokens.size(); t++) {
      |                      ~~^~~~~~~~~~~~~~~
mmcollapse.cpp: In function ‘int main(int, char**)’:
mmcollapse.cpp:632:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  632 |   for(int i=1; i < basenames.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~
mmcollapse.cpp:691:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  691 |   for(int s=0; s < basenames.size(); s++) {
      |                ~~^~~~~~~~~~~~~~~~~~
mmcollapse.cpp:707:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  707 |   for(int i=0; i < candidates.size(); i++) ts.push_back(i);
      |                ~~^~~~~~~~~~~~~~~~~~~
mmcollapse.cpp:732:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  732 |     for(int i=0 ;i < maxcorrs.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:738:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  738 |     for(int i=0 ;i < mincorrs.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:802:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  802 |         for(int i=0 ;i < maxcorrs.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:808:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  808 |         for(int i=0 ;i < mincorrs.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:827:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  827 |   for(int s=0; s < basenames.size(); s++) {
      |                ~~^~~~~~~~~~~~~~~~~~
mmcollapse.cpp:852:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  852 |       for(int t=0; t < tokens.size(); t++) {
      |                    ~~^~~~~~~~~~~~~~~
mmcollapse.cpp:882:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  882 |       for(int t=0; t < tokens2.size(); t++) {
      |                    ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:934:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  934 |     for(int t=0; t < M.n_cols; t++) {
      |                  ~~^~~~~~~~~~
mmcollapse.cpp:963:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  963 |     for(int i=1; i < tokens2.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:976:21: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  976 |       if(MM.size1() < i+1 ) factor1=2;
      |          ~~~~~~~~~~~^~~~~
mmcollapse.cpp:977:21: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  977 |       if(MM.size2() < j+1 ) factor2=2;
      |          ~~~~~~~~~~~^~~~~
mmcollapse.cpp:1010:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1010 |     for(int t=0; t < ids.size(); t++) {
      |                  ~~^~~~~~~~~~~~
mmcollapse.cpp:1083:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1083 |     for(int i=0; i < ids.size(); i++) {
      |                  ~~^~~~~~~~~~~~
mmcollapse.cpp:1092:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1092 |     for(int v = 0; v < M.n_cols; v++) {
      |                    ~~^~~~~~~~~~
mmcollapse.cpp:840:9: warning: unused variable ‘isident’ [-Wunused-variable]
  840 |     int isident=0;
      |         ^~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema0()’:
hitsio.cpp:163:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  163 |         for(int i = 0; i < transcriptName.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema0()’:
hitsio.cpp:184:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  184 |         for(int i = 0; i < currentReadTranscripts.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema1()’:
hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   24 |         if (VAL > numeric_limits<uint32_t>::max()) { \
      |                 ^
hitsio.cpp:191:9: note: in expansion of macro ‘WRITE_UINT’
  191 |         WRITE_UINT(ofs, hitsfileSchema);
      |         ^~~~~~~~~~
hitsio.cpp:193:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  193 |         for(int i = 0; i < transcriptName.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘std::map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
   24 |         if (VAL > numeric_limits<uint32_t>::max()) { \
hitsio.cpp:196:17: note: in expansion of macro ‘WRITE_UINT’
  196 |                 WRITE_UINT(ofs, transcriptTrueLength[transcriptName[i] ])
      |                 ^~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema1()’:
hitsio.cpp:236:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  236 |         for(int i = 0; i < currentReadTranscripts.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileReader::readHeaderSchema1(std::vector<std::__cxx11::basic_string<char> >*, std::map<std::__cxx11::basic_string<char>, double>*, std::map<std::__cxx11::basic_string<char>, int>*, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >*, std::vector<std::vector<std::__cxx11::basic_string<char> > >*)’:
hitsio.cpp:356:16: warning: unused variable ‘nextStrLen’ [-Wunused-variable]
  356 |         size_t nextStrLen;
      |                ^~~~~~~~~~
hitsio.cpp: In member function ‘bool HitsfileReader::readReadMapRecordTranscriptID(std::string&)’:
hitsio.cpp:447:1: warning: control reaches end of non-void function [-Wreturn-type]
  447 | }
      | ^
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -fopenmp -O3 sokal.o uh.o hitsio.o mmseq.cpp -o ../bin/mmseq -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -fopenmp -O3 fasta.o hitsio.o bam2hits.cpp -o ../bin/bam2hits -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
mmseq.cpp: In function ‘std::vector<double> meanvar(std::vector<double>, double, double)’:
mmseq.cpp:130:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  130 |   for(int i=0;i < v.size(); i++) {
      |               ~~^~~~~~~~~~
mmseq.cpp: In function ‘int main(int, char**)’:
mmseq.cpp:244:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  244 |       for(int i=0; i < tokens.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~
mmseq.cpp:423:20: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  423 |       if(M.size1() < m ) factor1=2;
      |          ~~~~~~~~~~^~~
mmseq.cpp:424:20: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  424 |       if(M.size2() < n ) factor2=2;
      |          ~~~~~~~~~~^~~
mmseq.cpp:594:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  594 |   for(unsigned t=0; t < n; t++)  {
      |                     ~~^~~
mmseq.cpp:736:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  736 |     for(unsigned t=0; t < n; t++)
      |                       ~~^~~
mmseq.cpp:765:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  765 |       for(unsigned t=0; t < n; t++)
      |                         ~~^~~
mmseq.cpp:801:50: warning: ‘-’ operator for reductions deprecated in OpenMP 5.2 [-Wdeprecated-openmp]
  801 |       #pragma omp for schedule(static) reduction(-:loglik_temp)
      |                                                  ^
      |                                                  +
mmseq.cpp:774:11: warning: unused variable ‘threadid’ [-Wunused-variable]
  774 |       int threadid=OMP_GET_THREAD_NUM;
      |           ^~~~~~~~
mmseq.cpp:829:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  829 |   for(unsigned t=0; t < n; t++)
      |                     ~~^~~
mmseq.cpp:912:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  912 |       for(unsigned t=0; t < n; t++) {
      |                         ~~^~~
mmseq.cpp:940:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  940 |   for(int i=0; i < identical_transcripts.size() * trace_length; i++) mu_trace_identical[i]=0;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:961:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  961 |   for(int i=0; i < gene2transcripts.size() * trace_length; i++) mu_trace_gene[i]=0;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1098:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1098 |   for(unsigned t=0; t < n; t++) gofs << indexSid[t] << " ";
      |                     ~~^~~
mmseq.cpp:1112:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1112 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1136:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1136 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1144:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1144 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1149:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1149 |   for(int i=0;i < identical_transcripts.size(); i++) {
      |               ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1156:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1156 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1161:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1161 |   for(int i=0;i < gene2transcripts.size(); i++) {
      |               ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1168:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1168 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1179:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1179 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1189:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1189 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1208:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1208 |     for(int t=0; t < identical_transcripts.size() ; t++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1212:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1212 |     for(int t=0; t < gene2transcripts.size(); t++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1226:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1226 |   for(int i=0; i < identical_transcripts.size() ; i++) meanmu_identical[i] /= trace_length;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1227:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1227 |   for(int i=0; i < gene2transcripts.size(); i++) meanmu_gene[i]/= trace_length;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1330:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1330 |   for(int t=0; t < identical_transcripts.size(); t++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1349:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1349 |   for(int g=0; g < gene2transcripts.size(); g++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1473:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1473 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1475:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1475 |     if(i==percentiles.size()-1) {
      |        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1482:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1482 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1484:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1484 |     if(i==percentiles.size()-1) {
      |        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1506:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1506 |       for(int i=0; i < percentiles.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1508:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1508 |         if(i==percentiles.size()-1) {
      |            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1514:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1514 |       for(int i=0; i < percentiles.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1516:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1516 |         if(i==percentiles.size()-1) {
      |            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1536:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1536 |       for(int i=0; i < percentiles.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1538:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1538 |         if(i==percentiles.size()-1) {
      |            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1544:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1544 |       for(int i=0; i < percentiles.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1546:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1546 |         if(i==percentiles.size()-1) {
      |            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1560:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1560 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1562:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1562 |     if(i==percentiles.size()-1) {
      |        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1582:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1582 |         for(int i=0; i < percentiles.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1584:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1584 |           if(i==percentiles.size()-1) {
      |              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1599:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1599 |         for(int i=0; i < percentiles.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1601:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1601 |           if(i==percentiles.size()-1) {
      |              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1619:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1619 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1621:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1621 |     if(i==percentiles.size()-1) {
      |        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1644:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1644 |         for(int i=0; i < percentiles.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1646:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1646 |           if(i==percentiles.size()-1) {
      |              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1656:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1656 |         for(int i=0; i < percentiles.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1658:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1658 |           if(i==percentiles.size()-1) {
      |              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:308:8: warning: unused variable ‘buf16384’ [-Wunused-variable]
  308 |   char buf16384[16384];
      |        ^~~~~~~~
mmseq.cpp:391:8: warning: variable ‘doublehit’ set but not used [-Wunused-but-set-variable=]
  391 |   bool doublehit;
      |        ^~~~~~~~~
bam2hits.cpp: In function ‘void outputMergeHeaders(std::vector<FastaRecord>&, char, const char*, bool, HitsfileWriter&)’:
bam2hits.cpp:109:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  109 |   for(int i=0; i < sortedfastas.size()-1; i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:119:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  119 |       for(int j=0; j < curSet.size()-1; j++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:137:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  137 |   for(int j=0; j < curSet.size()-1; j++) {
      |                ~~^~~~~~~~~~~~~~~~~
bam2hits.cpp: In function ‘std::vector<Alignment> repetitiveTranscriptFilter(std::vector<Alignment>&, int)’:
bam2hits.cpp:218:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Alignment>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  218 |   for(int j=0; j < alns.size(); j++) {
      |                ~~^~~~~~~~~~~~~
bam2hits.cpp:219:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  219 |     if(i < torem.size() && j==torem[i]) {
      |        ~~^~~~~~~~~~~~~~
bam2hits.cpp: In function ‘int main(int, char**)’:
bam2hits.cpp:518:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  518 |         if(_B != tg[0].size()-2) {
      |            ~~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:520:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  520 |           if(_A == tg[0].size()-2) {
      |              ~~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:522:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  522 |             if(_A != tg[1].size()-2) {
      |                ~~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:558:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  558 |       for(int i=1; i < tokens2.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~
bam2hits.cpp:609:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  609 |     for(int i=0; i < fastas.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~
bam2hits.cpp:645:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  645 |     for(int i=0;i < fastas.size(); i++) transcriptCounts[i] /= (double)fastas[i].seq().size();
      |                 ~~^~~~~~~~~~~~~~~
bam2hits.cpp:659:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  659 |     for(int i=0; i < fastas.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~
bam2hits.cpp:662:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  662 |         for(int j =0; j < fastas[i].seq().size(); j++) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:663:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  663 |           int tag = (j <= MSEQ_BEFORE || j >= fastas[i].seq().size()-MSEQ_AFTER) ? -2 : 0;
      |                                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:791:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  791 |       for(int j=MSEQ_BEFORE + 1; j <= fastas[i].seq().length()-MSEQ_AFTER; j++) {
      |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:920:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  920 |     for(int j=1; j < frequencies.size()-WINDOWFORISIZEMODE + 1; j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:948:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  948 |     for(int i=0; i < testIsizes.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~
bam2hits.cpp:959:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  959 |     for(int i=0; i < heights.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~
bam2hits.cpp:910:9: warning: variable ‘total’ set but not used [-Wunused-but-set-variable=]
  910 |     int total=0;
      |         ^~~~~
bam2hits.cpp:997:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  997 |       for(int fl=1; fl <= (it->seq()).size(); fl++) {
      |                     ~~~^~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:1091:56: warning: comparing the result of pointer addition ‘(bam_aux_get(((const bam1_t*)line), ((const char*)"NM")) + ((sizetype)ait.__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >::operator->()->Alignment::NM()))’ and NULL [-Waddress]
 1091 |             ait->NM(ait->NM() + bam_aux_get(line,"NM") == NULL ? 0 : bam_aux2i(bam_aux_get(line,"NM")));
      |                                                        ^
bms.cpp: In member function ‘arma::Col<int> BMS::m2v(arma::Mat<double>)’:
bms.cpp:36:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   36 |   for(int i=0; i < P.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:37:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   37 |     for(int j=0; j < P.n_rows; j++) {
      |                  ~~^~~~~~~~~~
bms.cpp: In member function ‘std::vector<double> BMS::meanvar(arma::Col<double>)’:
bms.cpp:76:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   76 |   for(int i=0;i < v.n_elem; i++) {
      |               ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::print(bool)’:
bms.cpp:93:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   93 |   for(int feature=0; feature < y->n_rows; feature++) {
      |                      ~~~~~~~~^~~~~~~~~~~
bms.cpp:97:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   97 |       for(int i=0; i < M.n_cols; i++) {
      |                    ~~^~~~~~~~~~
bms.cpp:102:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  102 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::printtune(int)’:
bms.cpp:132:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  132 |   for(int feature=0; feature < y->n_rows; feature++) {
      |                      ~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_alpha()’:
bms.cpp:185:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  185 |     for(int j=0; j < y->n_rows; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_beta()’:
bms.cpp:253:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  253 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:255:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  255 |       for(int b=0; b < M.n_cols; b++) {
      |                    ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_eta()’:
bms.cpp:332:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  332 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:334:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  334 |       for(int c=0; c < P[model].n_cols; c++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_sigmasq()’:
bms.cpp:415:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  415 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_lambda()’:
bms.cpp:504:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  504 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:506:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  506 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_rho()’:
bms.cpp:559:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  559 |     for(int j=0; j < y->n_rows; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::copy_pseudo()’:
bms.cpp:582:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  582 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:585:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  585 |     for(int c=0; c < P[0].n_cols; c++) {
      |                  ~~^~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_alpha(int, int, bool)’:
bms.cpp:603:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  603 |     for(int j=0; j < y->n_cols; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:610:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  610 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_beta(int, int, bool)’:
bms.cpp:631:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  631 |     for(int j=0; j < y->n_cols; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:638:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  638 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  646 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  651 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_eta(int, int, bool)’:
bms.cpp:663:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  663 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:666:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  666 |       for(int i=0; i < y->n_cols; i++) {
      |                    ~~^~~~~~~~~~~
bms.cpp:673:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  673 |       for(int i=0; i < y->n_cols; i++) {
      |                    ~~^~~~~~~~~~~
bms.cpp:681:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  681 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:686:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  686 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_lambda(int, int, bool)’:
bms.cpp:699:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  699 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:704:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  704 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:711:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  711 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_sigmasq(int, int, bool, bool)’:
bms.cpp:729:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  729 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:740:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  740 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:751:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  751 |         for(int i=0; i < y->n_cols; i++) {
      |                      ~~^~~~~~~~~~~
bms.cpp:763:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  763 |         for(int i=0; i < y->n_cols; i++) {
      |                      ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_sigmasq_RW(int, int, bool, bool)’:
bms.cpp:877:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  877 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘double BMS::log_target_posterior(int, int)’:
bms.cpp:931:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  931 |   for(int i=0; i < y->n_cols; i++) {
      |                ~~^~~~~~~~~~~
bms.cpp:940:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  940 |     for(int j=0; j < M.n_cols; j++) {
      |                  ~~^~~~~~~~~~
bms.cpp:947:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  947 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘double BMS::log_target_pseudo(int, int)’:
bms.cpp:968:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  968 |     for(int l=0; l < M.n_cols; l++) {
      |                  ~~^~~~~~~~~~
bms.cpp:974:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  974 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::print_pseudo()’:
bms.cpp:1086:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1086 |     for(int l=0; l < M.n_cols; l++) {
      |                  ~~^~~~~~~~~~
bms.cpp:1089:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1089 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:1100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1100 |   for(int i=0; i < y->n_rows; i++) {
      |                ~~^~~~~~~~~~~
bms.cpp:1103:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1103 |       for(int l=0; l < M.n_cols; l++) {
      |                    ~~^~~~~~~~~~
bms.cpp:1106:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1106 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In constructor ‘BMS::BMS(const arma::Mat<double>*, const arma::Mat<double>&, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<int>, double, double, double, std::string, gsl_rng**, int, bool)’:
bms.cpp:1188:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1188 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:1192:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1192 |         if(C(i,model)+1 > _n.size()) {
      |            ~~~~~~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::initialise_streams(std::string)’:
bms.cpp:1348:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1348 |   for(int i=0; i < M.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:1354:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1354 |   for(int i=0; i < M.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:1360:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1360 |   for(int i=0; i < P[0].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1366:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1366 |   for(int i=0; i < P[1].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1372:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1372 |   for(int i=0; i < P[0].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1378:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1378 |   for(int i=0; i < P[1].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -fopenmp -O3 hitsio.o hitstools.cpp -o ../bin/hitstools -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -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 -fopenmp -O2 bms.o mmdiff.cpp -o ../bin/mmdiff -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
hitstools.cpp: In function ‘void convert(char*, std::string)’:
hitstools.cpp:51:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   51 |         for(int i = 0; i < transcriptName.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~
hitstools.cpp: In function ‘int main(int, char**)’:
hitstools.cpp:96:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   96 |                 for(int i = 0; i < transcriptName.size(); i++) {
      |                                ~~^~~~~~~~~~~~~~~~~~~~~~~
hitstools.cpp:136:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  136 |     for(int i = 0; i < transcriptName.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp: In function ‘void parse_mmseq(std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, arma::Mat<double>&, arma::Mat<double>&, arma::Mat<double>&, int, int, double, bool)’:
mmdiff.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  100 |   for(int i=0; i < filenames.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:111:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  111 |     for(int j=0; j < tokens.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~
mmdiff.cpp:138:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  138 |       if(k + 1 > features.size()) {
      |          ~~~~~~^~~~~~~~~~~~~~~~~
mmdiff.cpp:147:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  147 |       if(k+1 > y.n_rows) {
      |          ~~~~^~~~~~~~~~
mmdiff.cpp:152:20: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  152 |       if(!useprops && tokens[lmg_ind]=="NA" || useprops && tokens[mp_ind]=="NA") {
      |          ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:173:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  173 |   if(range_start >=0 && range_end > range_start && range_end < y.n_rows) {
      |                                                    ~~~~~~~~~~^~~~~~~~~~
mmdiff.cpp:94:46: warning: variable ‘mcse_ind’ set but not used [-Wunused-but-set-variable=]
   94 |   int feature_ind=-1, lmg_ind=-1, sd_ind=-1, mcse_ind=-1, iact_ind=-1, mp_ind=-1, sp_ind=-1, uh_ind=-1;
      |                                              ^~~~~~~~
mmdiff.cpp:94:59: warning: variable ‘iact_ind’ set but not used [-Wunused-but-set-variable=]
   94 |   int feature_ind=-1, lmg_ind=-1, sd_ind=-1, mcse_ind=-1, iact_ind=-1, mp_ind=-1, sp_ind=-1, uh_ind=-1;
      |                                                           ^~~~~~~~
mmdiff.cpp: In function ‘void apply_normalisation(std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, arma::Mat<double>&, arma::Mat<double>&, double)’:
mmdiff.cpp:212:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  212 |   for(int i=0; i < uh.n_rows; i++) {
      |                ~~^~~~~~~~~~~
mmdiff.cpp:214:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  214 |     for(int j=0; j < uh.n_cols; j++) {
      |                  ~~^~~~~~~~~~~
mmdiff.cpp:230:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  230 |   for(int i=0; i < use.size(); i++) {
      |                ~~^~~~~~~~~~~~
mmdiff.cpp:232:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  232 |     for(int j=0; j < y.n_cols; j++) {
      |                  ~~^~~~~~~~~~
mmdiff.cpp:239:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  239 |   for(int sample=0; sample < y.n_cols; sample++) {
      |                     ~~~~~~~^~~~~~~~~~
mmdiff.cpp:241:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  241 |     for(int i=0; i < use.size(); i++) {
      |                  ~~^~~~~~~~~~~~
mmdiff.cpp:246:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  246 |     for(int i=0; i < y.n_rows; i++) {
      |                  ~~^~~~~~~~~~
mmdiff.cpp: In function ‘void apply_permutation(arma::Mat<double>&, arma::Mat<double>&)’:
mmdiff.cpp:257:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  257 |   for(int j=0; j< y.n_cols; j++) randinds.push_back(j);
      |                ~^~~~~~~~~~
mmdiff.cpp:258:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  258 |   for(int i=0; i < y.n_rows; i++) {
      |                ~~^~~~~~~~~~
mmdiff.cpp:259:19: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<int*, vector<int, allocator<int> > >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
  259 |     random_shuffle(randinds.begin(), randinds.end());
      |     ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/16/algorithm:63,
                 from mmdiff.cpp:31:
/usr/include/c++/16/bits/stl_algo.h:4515:5: note: declared here
 4515 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
      |     ^~~~~~~~~~~~~~
mmdiff.cpp:260:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  260 |     for(int j=0; j < y.n_cols; j++) {
      |                  ~~^~~~~~~~~~
mmdiff.cpp: In function ‘void parse_matrices(std::string, arma::Mat<double>&, arma::Mat<double>&, arma::Mat<double>&, arma::Mat<int>&, int)’:
mmdiff.cpp:310:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  310 |     for(int t=0; t < tokens.size(); t++) {
      |                  ~~^~~~~~~~~~~~~~~
mmdiff.cpp: In function ‘int main(int, char**)’:
mmdiff.cpp:420:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  420 |       for(int i=0; i < arguments.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:431:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  431 |       for(int i=0; i < arguments.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:439:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  439 |       while(ss < arguments.size()) {
      |             ~~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:451:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  451 |       if(ss != arguments.size()) {
      |          ~~~^~~~~~~~~~~~~~~~~~~
mmdiff.cpp:578:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  578 |   for(int i=0; i < arguments.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:640:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  640 |     for(int i=0; i < simple_de.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:759:17: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  759 |     if(inburnin && iter == OUTLEN/10 || !inburnin && iter==tuneiters) {
      |        ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:764:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  764 |     for(int feature=0; feature < features.size(); feature++) {
      |                        ~~~~~~~~^~~~~~~~~~~~~~~~~
mmdiff.cpp:837:17: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  837 |     if(inburnin && iter % subsample_burnin ==0 || !inburnin && iter >= tuneiters && (iter - tuneiters) % subsample_iter == 0) {
      |        ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:886:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  886 |       for(int l=0; l < M.n_cols; l++) {
      |                    ~~^~~~~~~~~~
mmdiff.cpp:898:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  898 |   for(int f=0; f < samplenames.size(); f++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:902:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  902 |       found2 = found2==string::npos ? -1 : found2;
      |                ~~~~~~^~~~~~~~~~~~~~
mmdiff.cpp:907:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  907 |   for(int f=0; f < samplenames.size(); f++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:909:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  909 |     if(f < samplenames.size()-1) cout << "\t";
      |        ~~^~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:914:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  914 |   for(int feature=0; feature < features.size(); feature++) {
      |                      ~~~~~~~~^~~~~~~~~~~~~~~~~
mmdiff.cpp:926:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  926 |         for(int l=0; l < M.n_cols; l++) {
      |                      ~~^~~~~~~~~~
mmdiff.cpp:936:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  936 |     for(int f=0; f < samplenames.size(); f++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:939:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  939 |     for(int f=0; f < samplenames.size(); f++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:941:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  941 |       if(f < samplenames.size()-1) cout << "\t";
      |          ~~^~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:951:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  951 |       for(int feature=0; feature < features.size(); feature++) {
      |                          ~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/bin/ld: /tmp/cck9Pusg.ltrans1.ltrans.o: in function `main':
/builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/src/bam2hits.cpp:653:(.text.startup+0x5a23): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Jzm8fp
+ umask 022
+ cd /builddir/build/BUILD/mmseq-1.0.11-build
+ '[' /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT
++ dirname /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build
+ mkdir /builddir/build/BUILD/mmseq-1.0.11-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 mmseq-1.0.11
+ rm -rf /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/bam2hits /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/extract_transcripts /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/hitstools /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/mmcollapse /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/mmdiff /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/mmseq /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/offsetGTF /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/t2g_hits /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/fastagrep.sh bin/mouse_strain_transcriptome.sh bin/usage.sh /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/filterGTF.rb bin/haploref.rb bin/testregexp.rb /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/ensembl_gtf_to_gff.pl /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.0.11-24.fc44 --unique-debug-suffix -1.0.11-24.fc44.x86_64 --unique-debug-src-base mmseq-1.0.11-24.fc44.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11
find-debuginfo: starting
Extracting debug info from 8 files
DWARF-compressing 8 files
sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/mmseq-1.0.11-24.fc44.x86_64
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ COMPRESS='gzip -9 -n'
+ COMPRESS_EXT=.gz
+ /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
mangling shebang in /usr/bin/ensembl_gtf_to_gff.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/testregexp.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/bin/haploref.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/bin/filterGTF.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/bin/usage.sh from /bin/bash to #!/usr/bin/bash
mangling shebang in /usr/bin/mouse_strain_transcriptome.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/fastagrep.sh from /bin/bash to #!/usr/bin/bash
+ /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/mmseq-1.0.11-build/BUILDROOT
Scanned 12 directories and 40 files,
    processed 0 inodes,
    0 modified (0 replaced + 0 rewritten),
    0 unsupported format, 0 errors
+ /usr/bin/linkdupes --brp /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr
Scanned 11 directories and 40 files,
    considered 40 files, read 0 files, linked 0 files, 0 errors
    sum of sizes of linked files: 0 bytes
Reading /builddir/build/BUILD/mmseq-1.0.11-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.Vp4aje
+ umask 022
+ cd /builddir/build/BUILD/mmseq-1.0.11-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 mmseq-1.0.11
++ bin/mmseq --version
++ true
+ test mmseq-1.0.11 = mmseq-1.0.11
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: mmseq-1.0.11-24.fc44.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.SLY6f2
+ umask 022
+ cd /builddir/build/BUILD/mmseq-1.0.11-build
+ cd mmseq-1.0.11
+ DOCDIR=/builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq
+ cp -pr /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/README.md /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq
+ cp -pr /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/COPYING /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq
+ cp -pr /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/doc /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: mmseq = 1.0.11-24.fc44 mmseq(x86-64) = 1.0.11-24.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/bash /usr/bin/perl /usr/bin/ruby /usr/bin/sh libboost_iostreams.so.1.83.0()(64bit) libboost_regex.so.1.83.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(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) libflexiblas.so.3()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgsl.so.28()(64bit) libgslcblas.so.0()(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) perl(strict) rtld(GNU_HASH)
Processing files: mmseq-debugsource-1.0.11-24.fc44.x86_64
Provides: mmseq-debugsource = 1.0.11-24.fc44 mmseq-debugsource(x86-64) = 1.0.11-24.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: mmseq-debuginfo-1.0.11-24.fc44.x86_64
Provides: debuginfo(build-id) = 35dccfc34000db7c44a606ea351e7a370ab466e4 debuginfo(build-id) = 5779dfc3f661fd89e96bde4a14f63cb0e7ce9e04 debuginfo(build-id) = 687593a979c0a5f69d13483959e2cafb7ba8fae1 debuginfo(build-id) = 8b98634b85837ccf2314926332680462de0a3725 debuginfo(build-id) = a8e16682e35114e5b19e0e34e5a051089c2ee50c debuginfo(build-id) = d0013a6f0539a21e01f8fbc042083ca29a93be6e debuginfo(build-id) = d367f0c7c4b40dfc4ee23556b8b92c02ed7f18b9 debuginfo(build-id) = f0963439ac37a4feb3ddfeda7ab4bde8b79b8c5a mmseq-debuginfo = 1.0.11-24.fc44 mmseq-debuginfo(x86-64) = 1.0.11-24.fc44
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: mmseq-debugsource(x86-64) = 1.0.11-24.fc44
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT
Wrote: /builddir/build/RPMS/mmseq-debugsource-1.0.11-24.fc44.x86_64.rpm
Wrote: /builddir/build/RPMS/mmseq-1.0.11-24.fc44.x86_64.rpm
Wrote: /builddir/build/RPMS/mmseq-debuginfo-1.0.11-24.fc44.x86_64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.UprH91
+ umask 022
+ cd /builddir/build/BUILD/mmseq-1.0.11-build
+ test -d /builddir/build/BUILD/mmseq-1.0.11-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/mmseq-1.0.11-build
+ rm -rf /builddir/build/BUILD/mmseq-1.0.11-build
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild mmseq-1.0.11-24.fc44.src.rpm
Finish: build phase for mmseq-1.0.11-24.fc44.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1767054237.482716/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/mmseq-1.0.11-24.fc44.src.rpm) Config(child) 1 minutes 21 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": "mmseq",
            "epoch": null,
            "version": "1.0.11",
            "release": "24.fc44",
            "arch": "x86_64"
        },
        {
            "name": "mmseq",
            "epoch": null,
            "version": "1.0.11",
            "release": "24.fc44",
            "arch": "src"
        },
        {
            "name": "mmseq-debuginfo",
            "epoch": null,
            "version": "1.0.11",
            "release": "24.fc44",
            "arch": "x86_64"
        },
        {
            "name": "mmseq-debugsource",
            "epoch": null,
            "version": "1.0.11",
            "release": "24.fc44",
            "arch": "x86_64"
        }
    ]
}
RPMResults finished