Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c1c9' (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/8598085-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64


Version: 1.2
PID: 9409
Logging PID: 9410
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': True,
 'build_id': 8598085,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': 'eb8d66331d804bbf2aa63420f219619041498140',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/orion/gsl-update/mmseq',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'mmseq',
 'package_version': '1.0.11-22',
 'project_dirname': 'gsl-update',
 'project_name': 'gsl-update',
 'project_owner': 'orion',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/orion/gsl-update/fedora-rawhide-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'orion/gsl-update--orion',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'storage': 0,
 'submitter': 'orion',
 'tags': [],
 'task_id': '8598085-fedora-rawhide-x86_64',
 'timeout': 96000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/orion/gsl-update/mmseq /var/lib/copr-rpmbuild/workspace/workdir-uvtf6f1v/mmseq --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/orion/gsl-update/mmseq', '/var/lib/copr-rpmbuild/workspace/workdir-uvtf6f1v/mmseq', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-uvtf6f1v/mmseq'...

Running: git checkout eb8d66331d804bbf2aa63420f219619041498140 --

cmd: ['git', 'checkout', 'eb8d66331d804bbf2aa63420f219619041498140', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-uvtf6f1v/mmseq
rc: 0
stdout: 
stderr: Note: switching to 'eb8d66331d804bbf2aa63420f219619041498140'.

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 eb8d663 automatic import of mmseq

Running: dist-git-client sources

cmd: ['dist-git-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-uvtf6f1v/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/orion/gsl-update/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  24.0M      0 --:--:-- --:--:-- --:--:-- 24.0M
INFO: Reading stdout from command: md5sum 1.0.11.zip

/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=96000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-uvtf6f1v/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-uvtf6f1v/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1738508284.648207 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 6.0 starting (python version = 3.13.0, NVR = mock-6.0-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-uvtf6f1v/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-uvtf6f1v/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1738508284.648207 -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-uvtf6f1v/mmseq/mmseq.spec)  Config(fedora-rawhide-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 6.0
INFO: Mock Version: 6.0
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1738508284.648207/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-d69da9a9-e3c2-4f5a-bf8d-d0feb81616d5
INFO: Checking that 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 image matches host's architecture
INFO: Copy content of container 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1738508284.648207/root
INFO: mounting 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 with podman image mount
INFO: image 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 as /var/lib/containers/storage/overlay/d3212d8beae72a97d426f4f4cbc9926037985c9d492b381ad2608549e5b9deb3/merged
INFO: umounting image 3b26c95bbe87cc88f475ce9c0ba4b394bf23541b10bebe9a634c9c8e61f73b10 (/var/lib/containers/storage/overlay/d3212d8beae72a97d426f4f4cbc9926037985c9d492b381ad2608549e5b9deb3/merged) with podman image umount
INFO: Removing image mock-bootstrap-d69da9a9-e3c2-4f5a-bf8d-d0feb81616d5
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_64-1738508284.648207/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf5 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.20.0-1.fc42.x86_64
  rpm-sequoia-1.7.0-3.fc42.x86_64
  dnf5-5.2.8.1-2.fc42.x86_64
  dnf5-plugins-5.2.8.1-2.fc42.x86_64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 fedora                                 100% |  13.3 MiB/s |  21.5 MiB |  00m02s
 Copr repository                        100% | 860.7 KiB/s |  56.8 KiB |  00m00s
Repositories loaded.
Package                            Arch   Version                    Repository      Size
Installing group/module packages:
 bash                              x86_64 5.2.37-1.fc42              fedora       8.2 MiB
 bzip2                             x86_64 1.0.8-20.fc42              fedora      99.3 KiB
 coreutils                         x86_64 9.6-1.fc42                 fedora       5.5 MiB
 cpio                              x86_64 2.15-2.fc41                fedora       1.1 MiB
 diffutils                         x86_64 3.10-9.fc42                fedora       1.6 MiB
 fedora-release-common             noarch 42-0.16                    fedora      19.8 KiB
 findutils                         x86_64 1:4.10.0-5.fc42            fedora       1.9 MiB
 gawk                              x86_64 5.3.1-1.fc42               fedora       1.7 MiB
 glibc-minimal-langpack            x86_64 2.40.9000-35.fc42          fedora       0.0   B
 grep                              x86_64 3.11-10.fc42               fedora       1.0 MiB
 gzip                              x86_64 1.13-3.fc42                fedora     392.9 KiB
 info                              x86_64 7.2-3.fc42                 fedora     357.9 KiB
 patch                             x86_64 2.7.6-26.fc42              fedora     258.7 KiB
 redhat-rpm-config                 noarch 342-1.fc42                 fedora     186.8 KiB
 rpm-build                         x86_64 4.20.0-8.fc42              fedora     165.2 KiB
 sed                               x86_64 4.9-4.fc42                 fedora     857.3 KiB
 shadow-utils                      x86_64 2:4.17.0-4.fc42            fedora       4.0 MiB
 tar                               x86_64 2:1.35-5.fc42              fedora       3.0 MiB
 unzip                             x86_64 6.0-66.fc42                fedora     390.3 KiB
 util-linux                        x86_64 2.40.4-2.fc42              fedora       3.4 MiB
 which                             x86_64 2.22-2.fc42                fedora      83.1 KiB
 xz                                x86_64 1:5.6.3-3.fc42             fedora       1.2 MiB
Installing dependencies:
 add-determinism                   x86_64 0.5.0-2.fc42               fedora       2.5 MiB
 alternatives                      x86_64 1.31-3.fc42                fedora      66.2 KiB
 ansible-srpm-macros               noarch 1-17.1.fc42                fedora      35.7 KiB
 audit-libs                        x86_64 4.0.3-2.fc42               fedora     351.3 KiB
 authselect                        x86_64 1.5.0-9.fc42               fedora     156.0 KiB
 authselect-libs                   x86_64 1.5.0-9.fc42               fedora     820.0 KiB
 basesystem                        noarch 11-22.fc42                 fedora       0.0   B
 binutils                          x86_64 2.43.50-12.fc42            fedora      25.8 MiB
 build-reproducibility-srpm-macros noarch 0.5.0-2.fc42               fedora     735.0   B
 bzip2-libs                        x86_64 1.0.8-20.fc42              fedora      84.6 KiB
 ca-certificates                   noarch 2024.2.69_v8.0.401-5.fc42  fedora       2.6 MiB
 coreutils-common                  x86_64 9.6-1.fc42                 fedora      11.1 MiB
 cracklib                          x86_64 2.9.11-7.fc42              fedora     242.4 KiB
 crypto-policies                   noarch 20250124-1.git4d262e7.fc42 fedora     137.4 KiB
 curl                              x86_64 8.11.1-3.fc42              fedora     454.7 KiB
 cyrus-sasl-lib                    x86_64 2.1.28-30.fc42             fedora       2.3 MiB
 dbus                              x86_64 1:1.16.0-3.fc42            fedora       0.0   B
 dbus-broker                       x86_64 36-5.fc42                  fedora     395.1 KiB
 dbus-common                       noarch 1:1.16.0-3.fc42            fedora      11.2 KiB
 debugedit                         x86_64 5.1-4.fc42                 fedora     200.4 KiB
 dwz                               x86_64 0.15-9.fc42                fedora     291.0 KiB
 ed                                x86_64 1.21-2.fc42                fedora     146.5 KiB
 efi-srpm-macros                   noarch 6-2.fc42                   fedora      40.1 KiB
 elfutils                          x86_64 0.192-8.fc42               fedora       2.7 MiB
 elfutils-debuginfod-client        x86_64 0.192-8.fc42               fedora      83.9 KiB
 elfutils-default-yama-scope       noarch 0.192-8.fc42               fedora       1.8 KiB
 elfutils-libelf                   x86_64 0.192-8.fc42               fedora       1.2 MiB
 elfutils-libs                     x86_64 0.192-8.fc42               fedora     675.0 KiB
 expat                             x86_64 2.6.4-2.fc42               fedora     292.8 KiB
 fedora-gpg-keys                   noarch 42-0.4                     fedora     128.2 KiB
 fedora-release                    noarch 42-0.16                    fedora       0.0   B
 fedora-release-identity-basic     noarch 42-0.16                    fedora     719.0   B
 fedora-repos                      noarch 42-0.4                     fedora       4.9 KiB
 fedora-repos-rawhide              noarch 42-0.4                     fedora       2.2 KiB
 file                              x86_64 5.45-9.fc42                fedora     103.4 KiB
 file-libs                         x86_64 5.45-9.fc42                fedora       9.9 MiB
 filesystem                        x86_64 3.18-36.fc42               fedora     112.0   B
 filesystem-srpm-macros            noarch 3.18-36.fc42               fedora      38.2 KiB
 fonts-srpm-macros                 noarch 1:2.0.5-21.fc42            fedora      55.8 KiB
 forge-srpm-macros                 noarch 0.4.0-2.fc42               fedora      38.9 KiB
 fpc-srpm-macros                   noarch 1.3-14.fc42                fedora     144.0   B
 gdb-minimal                       x86_64 15.2-7.fc42                fedora      13.0 MiB
 gdbm                              x86_64 1:1.23-9.fc42              fedora     460.3 KiB
 gdbm-libs                         x86_64 1:1.23-9.fc42              fedora     129.9 KiB
 ghc-srpm-macros                   noarch 1.9.2-2.fc42               fedora     779.0   B
 glibc                             x86_64 2.40.9000-35.fc42          fedora       6.6 MiB
 glibc-common                      x86_64 2.40.9000-35.fc42          fedora       1.0 MiB
 glibc-gconv-extra                 x86_64 2.40.9000-35.fc42          fedora       7.2 MiB
 gmp                               x86_64 1:6.3.0-2.fc41             fedora     811.4 KiB
 gnat-srpm-macros                  noarch 6-7.fc42                   fedora       1.0 KiB
 go-srpm-macros                    noarch 3.6.0-6.fc42               fedora      60.8 KiB
 jansson                           x86_64 2.14-2.fc42                fedora      93.1 KiB
 json-c                            x86_64 0.18-2.fc42                fedora      86.7 KiB
 kernel-srpm-macros                noarch 1.0-25.fc42                fedora       1.9 KiB
 keyutils-libs                     x86_64 1.6.3-5.fc42               fedora      58.3 KiB
 krb5-libs                         x86_64 1.21.3-5.fc42              fedora       2.3 MiB
 libacl                            x86_64 2.3.2-3.fc42               fedora      38.3 KiB
 libarchive                        x86_64 3.7.7-2.fc42               fedora     938.6 KiB
 libattr                           x86_64 2.5.2-5.fc42               fedora      27.1 KiB
 libblkid                          x86_64 2.40.4-2.fc42              fedora     262.4 KiB
 libbrotli                         x86_64 1.1.0-6.fc42               fedora     841.3 KiB
 libcap                            x86_64 2.73-2.fc42                fedora     207.1 KiB
 libcap-ng                         x86_64 0.8.5-4.fc42               fedora      72.9 KiB
 libcom_err                        x86_64 1.47.2-3.fc42              fedora      67.1 KiB
 libcurl                           x86_64 8.11.1-3.fc42              fedora     842.0 KiB
 libeconf                          x86_64 0.7.5-2.fc42               fedora      68.5 KiB
 libevent                          x86_64 2.1.12-15.fc42             fedora     903.1 KiB
 libfdisk                          x86_64 2.40.4-2.fc42              fedora     372.3 KiB
 libffi                            x86_64 3.4.6-5.fc42               fedora      82.3 KiB
 libgcc                            x86_64 15.0.1-0.5.fc42            fedora     266.6 KiB
 libgomp                           x86_64 15.0.1-0.5.fc42            fedora     535.6 KiB
 libidn2                           x86_64 2.3.7-3.fc42               fedora     329.0 KiB
 libmount                          x86_64 2.40.4-2.fc42              fedora     356.2 KiB
 libnghttp2                        x86_64 1.64.0-3.fc42              fedora     170.4 KiB
 libnsl2                           x86_64 2.0.1-3.fc42               fedora      57.9 KiB
 libpkgconf                        x86_64 2.3.0-2.fc42               fedora      78.1 KiB
 libpsl                            x86_64 0.21.5-5.fc42              fedora      76.4 KiB
 libpwquality                      x86_64 1.4.5-12.fc42              fedora     409.3 KiB
 libseccomp                        x86_64 2.5.5-2.fc41               fedora     173.3 KiB
 libselinux                        x86_64 3.8-1.fc42                 fedora     193.1 KiB
 libsemanage                       x86_64 3.8-1.fc42                 fedora     308.4 KiB
 libsepol                          x86_64 3.8-1.fc42                 fedora     826.0 KiB
 libsmartcols                      x86_64 2.40.4-2.fc42              fedora     180.4 KiB
 libssh                            x86_64 0.11.1-4.fc42              fedora     565.5 KiB
 libssh-config                     noarch 0.11.1-4.fc42              fedora     277.0   B
 libstdc++                         x86_64 15.0.1-0.5.fc42            fedora       2.8 MiB
 libtasn1                          x86_64 4.19.0-11.fc42             fedora     175.6 KiB
 libtirpc                          x86_64 1.3.6-1.rc3.fc42.2         fedora     199.0 KiB
 libtool-ltdl                      x86_64 2.5.4-4.fc42               fedora      70.1 KiB
 libunistring                      x86_64 1.1-9.fc42                 fedora       1.7 MiB
 libuuid                           x86_64 2.40.4-2.fc42              fedora      37.3 KiB
 libverto                          x86_64 0.3.2-10.fc42              fedora      25.4 KiB
 libxcrypt                         x86_64 4.4.38-4.fc42              fedora     268.0 KiB
 libxml2                           x86_64 2.12.9-2.fc42              fedora       1.7 MiB
 libzstd                           x86_64 1.5.6-3.fc42               fedora     795.8 KiB
 lua-libs                          x86_64 5.4.7-2.fc42               fedora     280.9 KiB
 lua-srpm-macros                   noarch 1-15.fc42                  fedora       1.3 KiB
 lz4-libs                          x86_64 1.10.0-2.fc42              fedora     157.4 KiB
 mpfr                              x86_64 4.2.1-6.fc42               fedora     831.9 KiB
 ncurses-base                      noarch 6.5-5.20250125.fc42        fedora     326.8 KiB
 ncurses-libs                      x86_64 6.5-5.20250125.fc42        fedora     946.3 KiB
 ocaml-srpm-macros                 noarch 10-4.fc42                  fedora       1.9 KiB
 openblas-srpm-macros              noarch 2-19.fc42                  fedora     112.0   B
 openldap                          x86_64 2.6.9-3.fc42               fedora     655.1 KiB
 openssl-libs                      x86_64 1:3.2.2-14.fc42            fedora       7.8 MiB
 p11-kit                           x86_64 0.25.5-5.fc42              fedora       2.2 MiB
 p11-kit-trust                     x86_64 0.25.5-5.fc42              fedora     395.5 KiB
 package-notes-srpm-macros         noarch 0.5-13.fc42                fedora       1.6 KiB
 pam                               x86_64 1.7.0-4.fc42               fedora       1.6 MiB
 pam-libs                          x86_64 1.7.0-4.fc42               fedora     126.7 KiB
 pcre2                             x86_64 10.44-1.fc42.2             fedora     649.3 KiB
 pcre2-syntax                      noarch 10.44-1.fc42.2             fedora     251.6 KiB
 perl-srpm-macros                  noarch 1-57.fc42                  fedora     861.0   B
 pkgconf                           x86_64 2.3.0-2.fc42               fedora      88.5 KiB
 pkgconf-m4                        noarch 2.3.0-2.fc42               fedora      14.4 KiB
 pkgconf-pkg-config                x86_64 2.3.0-2.fc42               fedora     989.0   B
 popt                              x86_64 1.19-8.fc42                fedora     132.8 KiB
 publicsuffix-list-dafsa           noarch 20250116-1.fc42            fedora      68.5 KiB
 pyproject-srpm-macros             noarch 1.16.4-2.fc42              fedora       1.9 KiB
 python-srpm-macros                noarch 3.13-4.fc42                fedora      51.0 KiB
 qt5-srpm-macros                   noarch 5.15.15-1.fc42             fedora     500.0   B
 qt6-srpm-macros                   noarch 6.8.1-5.fc42               fedora     456.0   B
 readline                          x86_64 8.2-12.fc42                fedora     485.0 KiB
 rpm                               x86_64 4.20.0-8.fc42              fedora       3.0 MiB
 rpm-build-libs                    x86_64 4.20.0-8.fc42              fedora     202.6 KiB
 rpm-libs                          x86_64 4.20.0-8.fc42              fedora     721.8 KiB
 rpm-sequoia                       x86_64 1.7.0-4.fc42               fedora       2.4 MiB
 rust-srpm-macros                  noarch 26.3-4.fc42                fedora       4.8 KiB
 setup                             noarch 2.15.0-10.fc42             fedora     720.7 KiB
 sqlite-libs                       x86_64 3.47.2-2.fc42              fedora       1.5 MiB
 systemd                           x86_64 257.2-17.fc42              fedora      17.4 MiB
 systemd-libs                      x86_64 257.2-17.fc42              fedora       2.2 MiB
 systemd-pam                       x86_64 257.2-17.fc42              fedora       1.1 MiB
 systemd-rpm-macros                noarch 257.2-17.fc42              fedora      10.7 KiB
 util-linux-core                   x86_64 2.40.4-2.fc42              fedora       1.4 MiB
 xxhash-libs                       x86_64 0.8.3-2.fc42               fedora      90.2 KiB
 xz-libs                           x86_64 1:5.6.3-3.fc42             fedora     218.3 KiB
 zig-srpm-macros                   noarch 1-4.fc42                   fedora       1.1 KiB
 zip                               x86_64 3.0-43.fc42                fedora     698.5 KiB
 zlib-ng-compat                    x86_64 2.2.3-2.fc42               fedora     137.6 KiB
 zstd                              x86_64 1.5.6-3.fc42               fedora       1.7 MiB
Installing groups:
 Buildsystem building group                                                              

Transaction Summary:
 Installing:       163 packages

Total size of inbound packages is 60 MiB. Need to download 60 MiB.
After this operation, 197 MiB extra will be used (install 197 MiB, remove 0 B).
[  1/163] bzip2-0:1.0.8-20.fc42.x86_64  100% | 165.8 KiB/s |  52.1 KiB |  00m00s
[  2/163] cpio-0:2.15-2.fc41.x86_64     100% |   1.1 MiB/s | 291.8 KiB |  00m00s
[  3/163] coreutils-0:9.6-1.fc42.x86_64 100% |   1.7 MiB/s |   1.2 MiB |  00m01s
[  4/163] bash-0:5.2.37-1.fc42.x86_64   100% |   2.6 MiB/s |   1.8 MiB |  00m01s
[  5/163] diffutils-0:3.10-9.fc42.x86_6 100% |   2.6 MiB/s | 404.6 KiB |  00m00s
[  6/163] fedora-release-common-0:42-0. 100% | 328.6 KiB/s |  24.3 KiB |  00m00s
[  7/163] findutils-1:4.10.0-5.fc42.x86 100% |   6.2 MiB/s | 551.5 KiB |  00m00s
[  8/163] glibc-minimal-langpack-0:2.40 100% |   1.5 MiB/s | 127.9 KiB |  00m00s
[  9/163] grep-0:3.11-10.fc42.x86_64    100% |   3.4 MiB/s | 300.1 KiB |  00m00s
[ 10/163] gzip-0:1.13-3.fc42.x86_64     100% |   2.2 MiB/s | 170.4 KiB |  00m00s
[ 11/163] info-0:7.2-3.fc42.x86_64      100% |   2.1 MiB/s | 183.8 KiB |  00m00s
[ 12/163] patch-0:2.7.6-26.fc42.x86_64  100% |   1.6 MiB/s | 128.4 KiB |  00m00s
[ 13/163] redhat-rpm-config-0:342-1.fc4 100% |   1.0 MiB/s |  81.6 KiB |  00m00s
[ 14/163] rpm-build-0:4.20.0-8.fc42.x86 100% |   1.0 MiB/s |  82.0 KiB |  00m00s
[ 15/163] sed-0:4.9-4.fc42.x86_64       100% |   3.6 MiB/s | 317.3 KiB |  00m00s
[ 16/163] shadow-utils-2:4.17.0-4.fc42. 100% |  11.9 MiB/s |   1.3 MiB |  00m00s
[ 17/163] unzip-0:6.0-66.fc42.x86_64    100% |   2.2 MiB/s | 184.6 KiB |  00m00s
[ 18/163] tar-2:1.35-5.fc42.x86_64      100% |   6.2 MiB/s | 862.5 KiB |  00m00s
[ 19/163] which-0:2.22-2.fc42.x86_64    100% | 568.5 KiB/s |  41.5 KiB |  00m00s
[ 20/163] util-linux-0:2.40.4-2.fc42.x8 100% |  10.9 MiB/s |   1.2 MiB |  00m00s
[ 21/163] xz-1:5.6.3-3.fc42.x86_64      100% |   3.0 MiB/s | 475.0 KiB |  00m00s
[ 22/163] gawk-0:5.3.1-1.fc42.x86_64    100% |   8.1 MiB/s |   1.1 MiB |  00m00s
[ 23/163] ncurses-libs-0:6.5-5.20250125 100% |   3.8 MiB/s | 335.0 KiB |  00m00s
[ 24/163] filesystem-0:3.18-36.fc42.x86 100% |  12.0 MiB/s |   1.3 MiB |  00m00s
[ 25/163] glibc-0:2.40.9000-35.fc42.x86 100% |  12.7 MiB/s |   2.3 MiB |  00m00s
[ 26/163] bzip2-libs-0:1.0.8-20.fc42.x8 100% | 581.0 KiB/s |  43.6 KiB |  00m00s
[ 27/163] coreutils-common-0:9.6-1.fc42 100% |  15.8 MiB/s |   2.1 MiB |  00m00s
[ 28/163] libacl-0:2.3.2-3.fc42.x86_64  100% | 310.9 KiB/s |  23.0 KiB |  00m00s
[ 29/163] gmp-1:6.3.0-2.fc41.x86_64     100% |   3.7 MiB/s | 318.0 KiB |  00m00s
[ 30/163] libattr-0:2.5.2-5.fc42.x86_64 100% | 237.3 KiB/s |  17.1 KiB |  00m00s
[ 31/163] libcap-0:2.73-2.fc42.x86_64   100% |   1.1 MiB/s |  84.3 KiB |  00m00s
[ 32/163] libselinux-0:3.8-1.fc42.x86_6 100% |   1.2 MiB/s |  97.1 KiB |  00m00s
[ 33/163] systemd-libs-0:257.2-17.fc42. 100% |   8.7 MiB/s | 819.3 KiB |  00m00s
[ 34/163] fedora-repos-0:42-0.4.noarch  100% | 120.5 KiB/s |   9.3 KiB |  00m00s
[ 35/163] openssl-libs-1:3.2.2-14.fc42. 100% |  17.8 MiB/s |   2.3 MiB |  00m00s
[ 36/163] pcre2-0:10.44-1.fc42.2.x86_64 100% |   3.0 MiB/s | 243.4 KiB |  00m00s
[ 37/163] glibc-common-0:2.40.9000-35.f 100% |   4.6 MiB/s | 415.4 KiB |  00m00s
[ 38/163] ed-0:1.21-2.fc42.x86_64       100% |   1.1 MiB/s |  82.0 KiB |  00m00s
[ 39/163] ansible-srpm-macros-0:1-17.1. 100% | 274.5 KiB/s |  20.3 KiB |  00m00s
[ 40/163] build-reproducibility-srpm-ma 100% | 159.0 KiB/s |  11.6 KiB |  00m00s
[ 41/163] dwz-0:0.15-9.fc42.x86_64      100% |   1.8 MiB/s | 135.7 KiB |  00m00s
[ 42/163] efi-srpm-macros-0:6-2.fc42.no 100% | 278.0 KiB/s |  22.5 KiB |  00m00s
[ 43/163] file-0:5.45-9.fc42.x86_64     100% | 615.6 KiB/s |  48.6 KiB |  00m00s
[ 44/163] filesystem-srpm-macros-0:3.18 100% | 340.9 KiB/s |  25.6 KiB |  00m00s
[ 45/163] fonts-srpm-macros-1:2.0.5-21. 100% | 361.3 KiB/s |  27.1 KiB |  00m00s
[ 46/163] forge-srpm-macros-0:0.4.0-2.f 100% | 264.7 KiB/s |  19.9 KiB |  00m00s
[ 47/163] fpc-srpm-macros-0:1.3-14.fc42 100% | 105.5 KiB/s |   8.0 KiB |  00m00s
[ 48/163] ghc-srpm-macros-0:1.9.2-2.fc4 100% | 117.4 KiB/s |   9.2 KiB |  00m00s
[ 49/163] gnat-srpm-macros-0:6-7.fc42.n 100% | 116.4 KiB/s |   8.6 KiB |  00m00s
[ 50/163] go-srpm-macros-0:3.6.0-6.fc42 100% | 373.8 KiB/s |  27.7 KiB |  00m00s
[ 51/163] kernel-srpm-macros-0:1.0-25.f 100% | 133.4 KiB/s |   9.9 KiB |  00m00s
[ 52/163] lua-srpm-macros-0:1-15.fc42.n 100% | 123.8 KiB/s |   8.9 KiB |  00m00s
[ 53/163] ocaml-srpm-macros-0:10-4.fc42 100% | 127.8 KiB/s |   9.2 KiB |  00m00s
[ 54/163] openblas-srpm-macros-0:2-19.f 100% |  92.4 KiB/s |   7.8 KiB |  00m00s
[ 55/163] package-notes-srpm-macros-0:0 100% | 112.9 KiB/s |   9.3 KiB |  00m00s
[ 56/163] perl-srpm-macros-0:1-57.fc42. 100% | 103.7 KiB/s |   8.5 KiB |  00m00s
[ 57/163] python-srpm-macros-0:3.13-4.f 100% | 314.7 KiB/s |  23.0 KiB |  00m00s
[ 58/163] pyproject-srpm-macros-0:1.16. 100% | 189.7 KiB/s |  14.0 KiB |  00m00s
[ 59/163] qt5-srpm-macros-0:5.15.15-1.f 100% | 123.6 KiB/s |   8.9 KiB |  00m00s
[ 60/163] qt6-srpm-macros-0:6.8.1-5.fc4 100% | 129.8 KiB/s |   9.3 KiB |  00m00s
[ 61/163] rust-srpm-macros-0:26.3-4.fc4 100% | 160.3 KiB/s |  11.7 KiB |  00m00s
[ 62/163] rpm-0:4.20.0-8.fc42.x86_64    100% |   6.4 MiB/s | 545.8 KiB |  00m00s
[ 63/163] zig-srpm-macros-0:1-4.fc42.no 100% | 104.4 KiB/s |   8.2 KiB |  00m00s
[ 64/163] debugedit-0:5.1-4.fc42.x86_64 100% |   1.0 MiB/s |  78.9 KiB |  00m00s
[ 65/163] zip-0:3.0-43.fc42.x86_64      100% |   3.3 MiB/s | 263.5 KiB |  00m00s
[ 66/163] elfutils-libelf-0:0.192-8.fc4 100% |   2.5 MiB/s | 208.1 KiB |  00m00s
[ 67/163] libarchive-0:3.7.7-2.fc42.x86 100% |   4.9 MiB/s | 416.9 KiB |  00m00s
[ 68/163] elfutils-0:0.192-8.fc42.x86_6 100% |   5.4 MiB/s | 551.0 KiB |  00m00s
[ 69/163] popt-0:1.19-8.fc42.x86_64     100% | 879.2 KiB/s |  65.9 KiB |  00m00s
[ 70/163] readline-0:8.2-12.fc42.x86_64 100% |   2.7 MiB/s | 215.2 KiB |  00m00s
[ 71/163] rpm-build-libs-0:4.20.0-8.fc4 100% |   1.2 MiB/s |  98.6 KiB |  00m00s
[ 72/163] rpm-libs-0:4.20.0-8.fc42.x86_ 100% |   3.9 MiB/s | 313.7 KiB |  00m00s
[ 73/163] zstd-0:1.5.6-3.fc42.x86_64    100% |   5.8 MiB/s | 479.6 KiB |  00m00s
[ 74/163] audit-libs-0:4.0.3-2.fc42.x86 100% |   1.6 MiB/s | 125.3 KiB |  00m00s
[ 75/163] libeconf-0:0.7.5-2.fc42.x86_6 100% | 473.8 KiB/s |  35.1 KiB |  00m00s
[ 76/163] libsemanage-0:3.8-1.fc42.x86_ 100% |   1.6 MiB/s | 123.6 KiB |  00m00s
[ 77/163] libxcrypt-0:4.4.38-4.fc42.x86 100% |   1.5 MiB/s | 119.2 KiB |  00m00s
[ 78/163] pam-libs-0:1.7.0-4.fc42.x86_6 100% | 788.2 KiB/s |  58.3 KiB |  00m00s
[ 79/163] setup-0:2.15.0-10.fc42.noarch 100% |   2.1 MiB/s | 156.1 KiB |  00m00s
[ 80/163] xz-libs-1:5.6.3-3.fc42.x86_64 100% |   1.5 MiB/s | 113.4 KiB |  00m00s
[ 81/163] mpfr-0:4.2.1-6.fc42.x86_64    100% |   3.9 MiB/s | 348.5 KiB |  00m00s
[ 82/163] libblkid-0:2.40.4-2.fc42.x86_ 100% |   1.5 MiB/s | 126.2 KiB |  00m00s
[ 83/163] libcap-ng-0:0.8.5-4.fc42.x86_ 100% | 402.1 KiB/s |  32.2 KiB |  00m00s
[ 84/163] libfdisk-0:2.40.4-2.fc42.x86_ 100% |   2.0 MiB/s | 162.3 KiB |  00m00s
[ 85/163] libmount-0:2.40.4-2.fc42.x86_ 100% |   2.1 MiB/s | 158.7 KiB |  00m00s
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[ 87/163] libuuid-0:2.40.4-2.fc42.x86_6 100% | 372.4 KiB/s |  29.0 KiB |  00m00s
[ 88/163] zlib-ng-compat-0:2.2.3-2.fc42 100% |   1.0 MiB/s |  78.9 KiB |  00m00s
[ 89/163] util-linux-core-0:2.40.4-2.fc 100% |   6.3 MiB/s | 533.1 KiB |  00m00s
[ 90/163] basesystem-0:11-22.fc42.noarc 100% | 101.2 KiB/s |   7.3 KiB |  00m00s
[ 91/163] libgcc-0:15.0.1-0.5.fc42.x86_ 100% |   1.5 MiB/s | 113.4 KiB |  00m00s
[ 92/163] glibc-gconv-extra-0:2.40.9000 100% |  16.4 MiB/s |   1.7 MiB |  00m00s
[ 93/163] ncurses-base-0:6.5-5.20250125 100% |   1.1 MiB/s |  88.1 KiB |  00m00s
[ 94/163] libsepol-0:3.8-1.fc42.x86_64  100% |   4.3 MiB/s | 348.9 KiB |  00m00s
[ 95/163] ca-certificates-0:2024.2.69_v 100% |  10.3 MiB/s | 949.0 KiB |  00m00s
[ 96/163] crypto-policies-0:20250124-1. 100% |   1.3 MiB/s |  98.3 KiB |  00m00s
[ 97/163] fedora-gpg-keys-0:42-0.4.noar 100% |   1.8 MiB/s | 135.6 KiB |  00m00s
[ 98/163] fedora-repos-rawhide-0:42-0.4 100% | 118.0 KiB/s |   8.9 KiB |  00m00s
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[101/163] file-libs-0:5.45-9.fc42.x86_6 100% |   8.7 MiB/s | 763.9 KiB |  00m00s
[102/163] curl-0:8.11.1-3.fc42.x86_64   100% |   2.7 MiB/s | 222.8 KiB |  00m00s
[103/163] elfutils-libs-0:0.192-8.fc42. 100% |   3.3 MiB/s | 265.9 KiB |  00m00s
[104/163] elfutils-debuginfod-client-0: 100% | 628.1 KiB/s |  46.5 KiB |  00m00s
[105/163] libzstd-0:1.5.6-3.fc42.x86_64 100% |   3.5 MiB/s | 311.1 KiB |  00m00s
[106/163] lz4-libs-0:1.10.0-2.fc42.x86_ 100% |   1.0 MiB/s |  78.1 KiB |  00m00s
[107/163] libstdc++-0:15.0.1-0.5.fc42.x 100% |   4.5 MiB/s | 891.5 KiB |  00m00s
[108/163] libgomp-0:15.0.1-0.5.fc42.x86 100% |   4.3 MiB/s | 347.1 KiB |  00m00s
[109/163] lua-libs-0:5.4.7-2.fc42.x86_6 100% |   1.7 MiB/s | 133.0 KiB |  00m00s
[110/163] libxml2-0:2.12.9-2.fc42.x86_6 100% |   2.9 MiB/s | 696.0 KiB |  00m00s
[111/163] rpm-sequoia-0:1.7.0-4.fc42.x8 100% |   9.8 MiB/s | 911.3 KiB |  00m00s
[112/163] elfutils-default-yama-scope-0 100% | 168.0 KiB/s |  12.6 KiB |  00m00s
[113/163] sqlite-libs-0:3.47.2-2.fc42.x 100% |   7.0 MiB/s | 734.8 KiB |  00m00s
[114/163] json-c-0:0.18-2.fc42.x86_64   100% | 623.7 KiB/s |  44.9 KiB |  00m00s
[115/163] authselect-libs-0:1.5.0-9.fc4 100% |   2.8 MiB/s | 216.1 KiB |  00m00s
[116/163] pam-0:1.7.0-4.fc42.x86_64     100% |   5.7 MiB/s | 555.7 KiB |  00m00s
[117/163] authselect-0:1.5.0-9.fc42.x86 100% |   1.8 MiB/s | 144.6 KiB |  00m00s
[118/163] gdbm-libs-1:1.23-9.fc42.x86_6 100% | 695.4 KiB/s |  57.0 KiB |  00m00s
[119/163] libnsl2-0:2.0.1-3.fc42.x86_64 100% | 388.7 KiB/s |  29.5 KiB |  00m00s
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[122/163] cracklib-0:2.9.11-7.fc42.x86_ 100% |   1.2 MiB/s |  91.6 KiB |  00m00s
[123/163] libcom_err-0:1.47.2-3.fc42.x8 100% | 345.2 KiB/s |  26.9 KiB |  00m00s
[124/163] krb5-libs-0:1.21.3-5.fc42.x86 100% |   8.3 MiB/s | 764.7 KiB |  00m00s
[125/163] keyutils-libs-0:1.6.3-5.fc42. 100% | 432.0 KiB/s |  31.5 KiB |  00m00s
[126/163] libverto-0:0.3.2-10.fc42.x86_ 100% | 277.3 KiB/s |  20.8 KiB |  00m00s
[127/163] systemd-rpm-macros-0:257.2-17 100% | 465.6 KiB/s |  34.9 KiB |  00m00s
[128/163] dbus-1:1.16.0-3.fc42.x86_64   100% | 103.5 KiB/s |   7.8 KiB |  00m00s
[129/163] libseccomp-0:2.5.5-2.fc41.x86 100% | 911.4 KiB/s |  70.2 KiB |  00m00s
[130/163] systemd-0:257.2-17.fc42.x86_6 100% |  30.5 MiB/s |   5.9 MiB |  00m00s
[131/163] systemd-pam-0:257.2-17.fc42.x 100% |   5.0 MiB/s | 417.0 KiB |  00m00s
[132/163] dbus-broker-0:36-5.fc42.x86_6 100% |   2.2 MiB/s | 174.1 KiB |  00m00s
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[134/163] expat-0:2.6.4-2.fc42.x86_64   100% |   1.5 MiB/s | 114.7 KiB |  00m00s
[135/163] alternatives-0:1.31-3.fc42.x8 100% | 560.3 KiB/s |  40.9 KiB |  00m00s
[136/163] jansson-0:2.14-2.fc42.x86_64  100% | 617.8 KiB/s |  45.7 KiB |  00m00s
[137/163] pkgconf-pkg-config-0:2.3.0-2. 100% | 137.8 KiB/s |   9.9 KiB |  00m00s
[138/163] pkgconf-0:2.3.0-2.fc42.x86_64 100% | 606.6 KiB/s |  44.9 KiB |  00m00s
[139/163] pkgconf-m4-0:2.3.0-2.fc42.noa 100% | 197.7 KiB/s |  14.2 KiB |  00m00s
[140/163] binutils-0:2.43.50-12.fc42.x8 100% |  22.1 MiB/s |   5.8 MiB |  00m00s
[141/163] libpkgconf-0:2.3.0-2.fc42.x86 100% | 518.5 KiB/s |  38.4 KiB |  00m00s
[142/163] gdbm-1:1.23-9.fc42.x86_64     100% |   2.0 MiB/s | 150.8 KiB |  00m00s
[143/163] libffi-0:3.4.6-5.fc42.x86_64  100% | 554.6 KiB/s |  39.9 KiB |  00m00s
[144/163] p11-kit-0:0.25.5-5.fc42.x86_6 100% |   5.9 MiB/s | 491.7 KiB |  00m00s
[145/163] libtasn1-0:4.19.0-11.fc42.x86 100% |   1.0 MiB/s |  74.5 KiB |  00m00s
[146/163] fedora-release-0:42-0.16.noar 100% | 181.5 KiB/s |  13.4 KiB |  00m00s
[147/163] p11-kit-trust-0:0.25.5-5.fc42 100% | 914.2 KiB/s | 132.6 KiB |  00m00s
[148/163] xxhash-libs-0:0.8.3-2.fc42.x8 100% | 527.9 KiB/s |  39.1 KiB |  00m00s
[149/163] fedora-release-identity-basic 100% | 197.7 KiB/s |  14.2 KiB |  00m00s
[150/163] libcurl-0:8.11.1-3.fc42.x86_6 100% |   4.7 MiB/s | 376.9 KiB |  00m00s
[151/163] gdb-minimal-0:15.2-7.fc42.x86 100% |  19.6 MiB/s |   4.4 MiB |  00m00s
[152/163] libbrotli-0:1.1.0-6.fc42.x86_ 100% |   4.4 MiB/s | 339.8 KiB |  00m00s
[153/163] libidn2-0:2.3.7-3.fc42.x86_64 100% |   1.5 MiB/s | 118.0 KiB |  00m00s
[154/163] libnghttp2-0:1.64.0-3.fc42.x8 100% |   1.0 MiB/s |  77.7 KiB |  00m00s
[155/163] libpsl-0:0.21.5-5.fc42.x86_64 100% | 877.2 KiB/s |  64.0 KiB |  00m00s
[156/163] libssh-0:0.11.1-4.fc42.x86_64 100% |   3.0 MiB/s | 233.3 KiB |  00m00s
[157/163] openldap-0:2.6.9-3.fc42.x86_6 100% |   3.4 MiB/s | 260.2 KiB |  00m00s
[158/163] libunistring-0:1.1-9.fc42.x86 100% |   6.9 MiB/s | 542.5 KiB |  00m00s
[159/163] publicsuffix-list-dafsa-0:202 100% | 795.0 KiB/s |  58.8 KiB |  00m00s
[160/163] libssh-config-0:0.11.1-4.fc42 100% | 125.0 KiB/s |   9.0 KiB |  00m00s
[161/163] cyrus-sasl-lib-0:2.1.28-30.fc 100% |   9.7 MiB/s | 793.5 KiB |  00m00s
[162/163] libevent-0:2.1.12-15.fc42.x86 100% |   3.3 MiB/s | 260.2 KiB |  00m00s
[163/163] libtool-ltdl-0:2.5.4-4.fc42.x 100% | 502.4 KiB/s |  36.2 KiB |  00m00s
--------------------------------------------------------------------------------
[163/163] Total                         100% |  11.3 MiB/s |  60.0 MiB |  00m05s
Running transaction
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 0x105EF944:
 UserID     : "Fedora (42) <fedora-42-primary@fedoraproject.org>"
 Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-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.
[  1/165] Verify package files          100% | 718.0   B/s | 163.0   B |  00m00s
[  2/165] Prepare transaction           100% |   1.8 KiB/s | 163.0   B |  00m00s
[  3/165] Installing libgcc-0:15.0.1-0. 100% | 131.0 MiB/s | 268.3 KiB |  00m00s
[  4/165] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
[  5/165] Installing publicsuffix-list- 100% |  67.6 MiB/s |  69.2 KiB |  00m00s
[  6/165] Installing fedora-release-ide 100% |   0.0   B/s | 976.0   B |  00m00s
[  7/165] Installing fedora-repos-rawhi 100% |   2.4 MiB/s |   2.4 KiB |  00m00s
[  8/165] Installing fedora-gpg-keys-0: 100% |  19.0 MiB/s | 174.8 KiB |  00m00s
[  9/165] Installing fedora-repos-0:42- 100% |   0.0   B/s |   5.7 KiB |  00m00s
[ 10/165] Installing fedora-release-com 100% |  11.8 MiB/s |  24.1 KiB |  00m00s
[ 11/165] Installing fedora-release-0:4 100% |   0.0   B/s | 124.0   B |  00m00s
[ 12/165] Installing setup-0:2.15.0-10. 100% |  37.3 MiB/s | 726.5 KiB |  00m00s
>>> [RPM] /etc/hosts created as /etc/hosts.rpmnew
[ 13/165] Installing filesystem-0:3.18- 100% |   1.4 MiB/s | 212.4 KiB |  00m00s
[ 14/165] Installing basesystem-0:11-22 100% |   0.0   B/s | 124.0   B |  00m00s
[ 15/165] Installing pkgconf-m4-0:2.3.0 100% |  14.5 MiB/s |  14.8 KiB |  00m00s
[ 16/165] Installing pcre2-syntax-0:10. 100% | 124.1 MiB/s | 254.1 KiB |  00m00s
[ 17/165] Installing ncurses-base-0:6.5 100% |  38.2 MiB/s | 352.2 KiB |  00m00s
[ 18/165] Installing glibc-minimal-lang 100% |   0.0   B/s | 124.0   B |  00m00s
[ 19/165] Installing ncurses-libs-0:6.5 100% | 132.9 MiB/s | 952.8 KiB |  00m00s
[ 20/165] Installing glibc-0:2.40.9000- 100% | 147.9 MiB/s |   6.7 MiB |  00m00s
[ 21/165] Installing bash-0:5.2.37-1.fc 100% | 199.3 MiB/s |   8.2 MiB |  00m00s
[ 22/165] Installing glibc-common-0:2.4 100% |  51.0 MiB/s |   1.0 MiB |  00m00s
[ 23/165] Installing glibc-gconv-extra- 100% | 138.0 MiB/s |   7.3 MiB |  00m00s
[ 24/165] Installing zlib-ng-compat-0:2 100% | 135.2 MiB/s | 138.4 KiB |  00m00s
[ 25/165] Installing bzip2-libs-0:1.0.8 100% |  83.7 MiB/s |  85.7 KiB |  00m00s
[ 26/165] Installing xz-libs-1:5.6.3-3. 100% | 214.3 MiB/s | 219.4 KiB |  00m00s
[ 27/165] Installing popt-0:1.19-8.fc42 100% |  34.0 MiB/s | 139.4 KiB |  00m00s
[ 28/165] Installing readline-0:8.2-12. 100% | 237.9 MiB/s | 487.1 KiB |  00m00s
[ 29/165] Installing libxcrypt-0:4.4.38 100% | 132.2 MiB/s | 270.7 KiB |  00m00s
[ 30/165] Installing libuuid-0:2.40.4-2 100% |  37.5 MiB/s |  38.4 KiB |  00m00s
[ 31/165] Installing libblkid-0:2.40.4- 100% | 128.6 MiB/s | 263.4 KiB |  00m00s
[ 32/165] Installing gmp-1:6.3.0-2.fc41 100% | 198.6 MiB/s | 813.7 KiB |  00m00s
[ 33/165] Installing libstdc++-0:15.0.1 100% | 282.0 MiB/s |   2.8 MiB |  00m00s
[ 34/165] Installing libzstd-0:1.5.6-3. 100% | 259.5 MiB/s | 797.0 KiB |  00m00s
[ 35/165] Installing elfutils-libelf-0: 100% | 292.5 MiB/s |   1.2 MiB |  00m00s
[ 36/165] Installing libattr-0:2.5.2-5. 100% |  27.4 MiB/s |  28.1 KiB |  00m00s
[ 37/165] Installing libacl-0:2.3.2-3.f 100% |  38.2 MiB/s |  39.2 KiB |  00m00s
[ 38/165] Installing libeconf-0:0.7.5-2 100% |  68.5 MiB/s |  70.1 KiB |  00m00s
[ 39/165] Installing libcap-ng-0:0.8.5- 100% |  73.1 MiB/s |  74.8 KiB |  00m00s
[ 40/165] Installing audit-libs-0:4.0.3 100% | 172.6 MiB/s | 353.4 KiB |  00m00s
[ 41/165] Installing pam-libs-0:1.7.0-4 100% | 126.1 MiB/s | 129.1 KiB |  00m00s
[ 42/165] Installing libcap-0:2.73-2.fc 100% |  13.8 MiB/s | 212.1 KiB |  00m00s
[ 43/165] Installing systemd-libs-0:257 100% | 249.3 MiB/s |   2.2 MiB |  00m00s
[ 44/165] Installing gdbm-libs-1:1.23-9 100% | 128.5 MiB/s | 131.6 KiB |  00m00s
[ 45/165] Installing dwz-0:0.15-9.fc42. 100% |  22.0 MiB/s | 292.4 KiB |  00m00s
[ 46/165] Installing mpfr-0:4.2.1-6.fc4 100% | 203.5 MiB/s | 833.6 KiB |  00m00s
[ 47/165] Installing gawk-0:5.3.1-1.fc4 100% |  77.0 MiB/s |   1.7 MiB |  00m00s
[ 48/165] Installing libfdisk-0:2.40.4- 100% | 182.4 MiB/s | 373.5 KiB |  00m00s
[ 49/165] Installing unzip-0:6.0-66.fc4 100% |  27.5 MiB/s | 393.8 KiB |  00m00s
[ 50/165] Installing file-libs-0:5.45-9 100% | 473.2 MiB/s |   9.9 MiB |  00m00s
[ 51/165] Installing file-0:5.45-9.fc42 100% |   4.1 MiB/s | 104.8 KiB |  00m00s
[ 52/165] Installing crypto-policies-0: 100% |  14.5 MiB/s | 163.7 KiB |  00m00s
[ 53/165] Installing pcre2-0:10.44-1.fc 100% | 211.8 MiB/s | 650.7 KiB |  00m00s
[ 54/165] Installing grep-0:3.11-10.fc4 100% |  45.6 MiB/s |   1.0 MiB |  00m00s
[ 55/165] Installing xz-1:5.6.3-3.fc42. 100% |  58.5 MiB/s |   1.2 MiB |  00m00s
[ 56/165] Installing libsmartcols-0:2.4 100% | 177.2 MiB/s | 181.4 KiB |  00m00s
[ 57/165] Installing libsepol-0:3.8-1.f 100% | 201.9 MiB/s | 827.0 KiB |  00m00s
[ 58/165] Installing libselinux-0:3.8-1 100% |  94.9 MiB/s | 194.3 KiB |  00m00s
[ 59/165] Installing sed-0:4.9-4.fc42.x 100% |  44.5 MiB/s | 865.5 KiB |  00m00s
[ 60/165] Installing findutils-1:4.10.0 100% |  85.2 MiB/s |   1.9 MiB |  00m00s
[ 61/165] Installing libmount-0:2.40.4- 100% | 174.4 MiB/s | 357.2 KiB |  00m00s
[ 62/165] Installing util-linux-core-0: 100% |  62.0 MiB/s |   1.4 MiB |  00m00s
[ 63/165] Installing lz4-libs-0:1.10.0- 100% | 154.7 MiB/s | 158.5 KiB |  00m00s
[ 64/165] Installing lua-libs-0:5.4.7-2 100% | 137.7 MiB/s | 282.1 KiB |  00m00s
[ 65/165] Installing libcom_err-0:1.47. 100% |  66.6 MiB/s |  68.2 KiB |  00m00s
[ 66/165] Installing alternatives-0:1.3 100% |   5.1 MiB/s |  67.7 KiB |  00m00s
[ 67/165] Installing libffi-0:3.4.6-5.f 100% |  81.7 MiB/s |  83.7 KiB |  00m00s
[ 68/165] Installing libtasn1-0:4.19.0- 100% |  86.6 MiB/s | 177.4 KiB |  00m00s
[ 69/165] Installing p11-kit-0:0.25.5-5 100% |  84.0 MiB/s |   2.2 MiB |  00m00s
[ 70/165] Installing libunistring-0:1.1 100% | 246.7 MiB/s |   1.7 MiB |  00m00s
[ 71/165] Installing libidn2-0:2.3.7-3. 100% |  65.4 MiB/s | 335.0 KiB |  00m00s
[ 72/165] Installing libpsl-0:0.21.5-5. 100% |  75.7 MiB/s |  77.5 KiB |  00m00s
[ 73/165] Installing p11-kit-trust-0:0. 100% |  13.9 MiB/s | 397.2 KiB |  00m00s
[ 74/165] Installing zstd-0:1.5.6-3.fc4 100% |  84.8 MiB/s |   1.7 MiB |  00m00s
[ 75/165] Installing tar-2:1.35-5.fc42. 100% | 118.5 MiB/s |   3.0 MiB |  00m00s
[ 76/165] Installing libsemanage-0:3.8- 100% | 101.0 MiB/s | 310.2 KiB |  00m00s
[ 77/165] Installing shadow-utils-2:4.1 100% |  87.4 MiB/s |   4.0 MiB |  00m00s
[ 78/165] Installing zip-0:3.0-43.fc42. 100% |  42.9 MiB/s | 702.4 KiB |  00m00s
[ 79/165] Installing gdbm-1:1.23-9.fc42 100% |  28.4 MiB/s | 465.2 KiB |  00m00s
[ 80/165] Installing cyrus-sasl-lib-0:2 100% | 109.7 MiB/s |   2.3 MiB |  00m00s
[ 81/165] Installing libxml2-0:2.12.9-2 100% |  89.9 MiB/s |   1.7 MiB |  00m00s
[ 82/165] Installing bzip2-0:1.0.8-20.f 100% |   7.8 MiB/s | 103.8 KiB |  00m00s
[ 83/165] Installing add-determinism-0: 100% | 122.8 MiB/s |   2.5 MiB |  00m00s
[ 84/165] Installing build-reproducibil 100% |   0.0   B/s |   1.0 KiB |  00m00s
[ 85/165] Installing sqlite-libs-0:3.47 100% | 250.7 MiB/s |   1.5 MiB |  00m00s
[ 86/165] Installing ed-0:1.21-2.fc42.x 100% |  11.2 MiB/s | 148.8 KiB |  00m00s
[ 87/165] Installing patch-0:2.7.6-26.f 100% |  19.5 MiB/s | 260.2 KiB |  00m00s
[ 88/165] Installing filesystem-srpm-ma 100% |  38.0 MiB/s |  38.9 KiB |  00m00s
[ 89/165] Installing elfutils-default-y 100% | 185.7 KiB/s |   2.0 KiB |  00m00s
[ 90/165] Installing elfutils-libs-0:0. 100% | 165.2 MiB/s | 676.7 KiB |  00m00s
[ 91/165] Installing dbus-common-1:1.16 100% |   1.2 MiB/s |  13.6 KiB |  00m00s
[ 92/165] Installing cpio-0:2.15-2.fc41 100% |  50.0 MiB/s |   1.1 MiB |  00m00s
[ 93/165] Installing diffutils-0:3.10-9 100% |  75.7 MiB/s |   1.6 MiB |  00m00s
[ 94/165] Installing libgomp-0:15.0.1-0 100% | 262.2 MiB/s | 537.0 KiB |  00m00s
[ 95/165] Installing json-c-0:0.18-2.fc 100% |  85.9 MiB/s |  88.0 KiB |  00m00s
[ 96/165] Installing keyutils-libs-0:1. 100% |  58.3 MiB/s |  59.7 KiB |  00m00s
[ 97/165] Installing libverto-0:0.3.2-1 100% |  26.6 MiB/s |  27.2 KiB |  00m00s
[ 98/165] Installing libseccomp-0:2.5.5 100% |  85.5 MiB/s | 175.2 KiB |  00m00s
[ 99/165] Installing expat-0:2.6.4-2.fc 100% |   7.2 MiB/s | 294.9 KiB |  00m00s
[100/165] Installing dbus-broker-0:36-5 100% |  12.9 MiB/s | 397.6 KiB |  00m00s
[101/165] Installing dbus-1:1.16.0-3.fc 100% |   0.0   B/s | 124.0   B |  00m00s
[102/165] Installing jansson-0:2.14-2.f 100% |  92.2 MiB/s |  94.4 KiB |  00m00s
[103/165] Installing libpkgconf-0:2.3.0 100% |  77.4 MiB/s |  79.2 KiB |  00m00s
[104/165] Installing pkgconf-0:2.3.0-2. 100% |   6.3 MiB/s |  91.0 KiB |  00m00s
[105/165] Installing pkgconf-pkg-config 100% | 147.8 KiB/s |   1.8 KiB |  00m00s
[106/165] Installing xxhash-libs-0:0.8. 100% |  89.4 MiB/s |  91.6 KiB |  00m00s
[107/165] Installing libbrotli-0:1.1.0- 100% | 205.9 MiB/s | 843.6 KiB |  00m00s
[108/165] Installing libnghttp2-0:1.64. 100% | 167.5 MiB/s | 171.5 KiB |  00m00s
[109/165] Installing libtool-ltdl-0:2.5 100% |  69.6 MiB/s |  71.2 KiB |  00m00s
[110/165] Installing rust-srpm-macros-0 100% |   0.0   B/s |   5.6 KiB |  00m00s
[111/165] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 732.0   B |  00m00s
[112/165] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 776.0   B |  00m00s
[113/165] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[114/165] Installing package-notes-srpm 100% |   0.0   B/s |   2.0 KiB |  00m00s
[115/165] Installing openblas-srpm-macr 100% |   0.0   B/s | 392.0   B |  00m00s
[116/165] Installing ocaml-srpm-macros- 100% |   0.0   B/s |   2.2 KiB |  00m00s
[117/165] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[118/165] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[119/165] Installing ghc-srpm-macros-0: 100% |   0.0   B/s |   1.0 KiB |  00m00s
[120/165] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[121/165] Installing ansible-srpm-macro 100% |  35.4 MiB/s |  36.2 KiB |  00m00s
[122/165] Installing coreutils-common-0 100% | 247.9 MiB/s |  11.2 MiB |  00m00s
[123/165] Installing openssl-libs-1:3.2 100% | 301.4 MiB/s |   7.8 MiB |  00m00s
[124/165] Installing coreutils-0:9.6-1. 100% | 108.8 MiB/s |   5.5 MiB |  00m00s
[125/165] Installing ca-certificates-0: 100% |   1.2 MiB/s |   2.4 MiB |  00m02s
[126/165] Installing krb5-libs-0:1.21.3 100% | 191.6 MiB/s |   2.3 MiB |  00m00s
[127/165] Installing libarchive-0:3.7.7 100% | 229.6 MiB/s | 940.6 KiB |  00m00s
[128/165] Installing libtirpc-0:1.3.6-1 100% |  98.0 MiB/s | 200.7 KiB |  00m00s
[129/165] Installing gzip-0:1.13-3.fc42 100% |  24.3 MiB/s | 398.4 KiB |  00m00s
[130/165] Installing authselect-libs-0: 100% |  90.6 MiB/s | 835.0 KiB |  00m00s
[131/165] Installing cracklib-0:2.9.11- 100% |  13.0 MiB/s | 253.7 KiB |  00m00s
[132/165] Installing libpwquality-0:1.4 100% |  20.6 MiB/s | 421.6 KiB |  00m00s
[133/165] Installing libnsl2-0:2.0.1-3. 100% |  28.8 MiB/s |  59.0 KiB |  00m00s
[134/165] Installing pam-0:1.7.0-4.fc42 100% |  47.1 MiB/s |   1.7 MiB |  00m00s
[135/165] Installing util-linux-0:2.40. 100% |  64.1 MiB/s |   3.5 MiB |  00m00s
[136/165] Installing systemd-pam-0:257. 100% | 139.1 MiB/s |   1.1 MiB |  00m00s
[137/165] Installing systemd-0:257.2-17 100% |  61.7 MiB/s |  17.5 MiB |  00m00s
>>> Running post-install scriptlet: systemd-0:257.2-17.fc42.x86_64
>>> Finished post-install scriptlet: systemd-0:257.2-17.fc42.x86_64
>>> Scriptlet output:
>>> Creating group 'systemd-journal' with GID 190.
>>> Creating group 'systemd-oom' with GID 999.
>>> Creating user 'systemd-oom' (systemd Userspace OOM Killer) with UID 999 and 
>>> 
[138/165] Installing libssh-0:0.11.1-4. 100% | 138.6 MiB/s | 567.5 KiB |  00m00s
[139/165] Installing rpm-sequoia-0:1.7. 100% | 241.4 MiB/s |   2.4 MiB |  00m00s
[140/165] Installing rpm-libs-0:4.20.0- 100% | 100.9 MiB/s | 723.3 KiB |  00m00s
[141/165] Installing rpm-build-libs-0:4 100% |  99.3 MiB/s | 203.4 KiB |  00m00s
[142/165] Installing libevent-0:2.1.12- 100% | 177.1 MiB/s | 906.9 KiB |  00m00s
[143/165] Installing openldap-0:2.6.9-3 100% | 160.9 MiB/s | 658.9 KiB |  00m00s
[144/165] Installing libcurl-0:8.11.1-3 100% | 205.8 MiB/s | 843.1 KiB |  00m00s
[145/165] Installing elfutils-debuginfo 100% |   5.6 MiB/s |  86.2 KiB |  00m00s
[146/165] Installing elfutils-0:0.192-8 100% | 112.0 MiB/s |   2.7 MiB |  00m00s
[147/165] Installing binutils-0:2.43.50 100% | 232.9 MiB/s |  25.9 MiB |  00m00s
[148/165] Installing gdb-minimal-0:15.2 100% | 232.9 MiB/s |  13.0 MiB |  00m00s
[149/165] Installing debugedit-0:5.1-4. 100% |  13.2 MiB/s | 203.1 KiB |  00m00s
[150/165] Installing curl-0:8.11.1-3.fc 100% |  14.0 MiB/s | 457.1 KiB |  00m00s
[151/165] Installing rpm-0:4.20.0-8.fc4 100% |  60.7 MiB/s |   2.5 MiB |  00m00s
[152/165] Installing efi-srpm-macros-0: 100% |  40.1 MiB/s |  41.1 KiB |  00m00s
[153/165] Installing lua-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[154/165] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.7 KiB |  00m00s
[155/165] Installing fonts-srpm-macros- 100% |  55.7 MiB/s |  57.0 KiB |  00m00s
[156/165] Installing forge-srpm-macros- 100% |  39.3 MiB/s |  40.3 KiB |  00m00s
[157/165] Installing go-srpm-macros-0:3 100% |  60.5 MiB/s |  62.0 KiB |  00m00s
[158/165] Installing python-srpm-macros 100% |  50.9 MiB/s |  52.2 KiB |  00m00s
[159/165] Installing redhat-rpm-config- 100% |  47.2 MiB/s | 193.5 KiB |  00m00s
[160/165] Installing rpm-build-0:4.20.0 100% |  10.0 MiB/s | 173.7 KiB |  00m00s
[161/165] Installing pyproject-srpm-mac 100% |   2.4 MiB/s |   2.5 KiB |  00m00s
[162/165] Installing authselect-0:1.5.0 100% |  10.4 MiB/s | 160.4 KiB |  00m00s
[163/165] Installing which-0:2.22-2.fc4 100% |   6.4 MiB/s |  85.3 KiB |  00m00s
[164/165] Installing info-0:7.2-3.fc42. 100% |  21.9 MiB/s | 358.3 KiB |  00m00s
[165/165] Installing systemd-rpm-macros 100% |   4.0 KiB/s |  11.3 KiB |  00m03s
Public key "file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary" is already present, not importing.
Complete!
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: add-determinism-0.5.0-2.fc42.x86_64
alternatives-1.31-3.fc42.x86_64
ansible-srpm-macros-1-17.1.fc42.noarch
audit-libs-4.0.3-2.fc42.x86_64
authselect-1.5.0-9.fc42.x86_64
authselect-libs-1.5.0-9.fc42.x86_64
basesystem-11-22.fc42.noarch
bash-5.2.37-1.fc42.x86_64
binutils-2.43.50-12.fc42.x86_64
build-reproducibility-srpm-macros-0.5.0-2.fc42.noarch
bzip2-1.0.8-20.fc42.x86_64
bzip2-libs-1.0.8-20.fc42.x86_64
ca-certificates-2024.2.69_v8.0.401-5.fc42.noarch
coreutils-9.6-1.fc42.x86_64
coreutils-common-9.6-1.fc42.x86_64
cpio-2.15-2.fc41.x86_64
cracklib-2.9.11-7.fc42.x86_64
crypto-policies-20250124-1.git4d262e7.fc42.noarch
curl-8.11.1-3.fc42.x86_64
cyrus-sasl-lib-2.1.28-30.fc42.x86_64
dbus-1.16.0-3.fc42.x86_64
dbus-broker-36-5.fc42.x86_64
dbus-common-1.16.0-3.fc42.noarch
debugedit-5.1-4.fc42.x86_64
diffutils-3.10-9.fc42.x86_64
dwz-0.15-9.fc42.x86_64
ed-1.21-2.fc42.x86_64
efi-srpm-macros-6-2.fc42.noarch
elfutils-0.192-8.fc42.x86_64
elfutils-debuginfod-client-0.192-8.fc42.x86_64
elfutils-default-yama-scope-0.192-8.fc42.noarch
elfutils-libelf-0.192-8.fc42.x86_64
elfutils-libs-0.192-8.fc42.x86_64
expat-2.6.4-2.fc42.x86_64
fedora-gpg-keys-42-0.4.noarch
fedora-release-42-0.16.noarch
fedora-release-common-42-0.16.noarch
fedora-release-identity-basic-42-0.16.noarch
fedora-repos-42-0.4.noarch
fedora-repos-rawhide-42-0.4.noarch
file-5.45-9.fc42.x86_64
file-libs-5.45-9.fc42.x86_64
filesystem-3.18-36.fc42.x86_64
filesystem-srpm-macros-3.18-36.fc42.noarch
findutils-4.10.0-5.fc42.x86_64
fonts-srpm-macros-2.0.5-21.fc42.noarch
forge-srpm-macros-0.4.0-2.fc42.noarch
fpc-srpm-macros-1.3-14.fc42.noarch
gawk-5.3.1-1.fc42.x86_64
gdb-minimal-15.2-7.fc42.x86_64
gdbm-1.23-9.fc42.x86_64
gdbm-libs-1.23-9.fc42.x86_64
ghc-srpm-macros-1.9.2-2.fc42.noarch
glibc-2.40.9000-35.fc42.x86_64
glibc-common-2.40.9000-35.fc42.x86_64
glibc-gconv-extra-2.40.9000-35.fc42.x86_64
glibc-minimal-langpack-2.40.9000-35.fc42.x86_64
gmp-6.3.0-2.fc41.x86_64
gnat-srpm-macros-6-7.fc42.noarch
go-srpm-macros-3.6.0-6.fc42.noarch
gpg-pubkey-105ef944-65ca83d1
gpg-pubkey-31645531-66b6dccf
gpg-pubkey-6d9f90a6-6786af3b
grep-3.11-10.fc42.x86_64
gzip-1.13-3.fc42.x86_64
info-7.2-3.fc42.x86_64
jansson-2.14-2.fc42.x86_64
json-c-0.18-2.fc42.x86_64
kernel-srpm-macros-1.0-25.fc42.noarch
keyutils-libs-1.6.3-5.fc42.x86_64
krb5-libs-1.21.3-5.fc42.x86_64
libacl-2.3.2-3.fc42.x86_64
libarchive-3.7.7-2.fc42.x86_64
libattr-2.5.2-5.fc42.x86_64
libblkid-2.40.4-2.fc42.x86_64
libbrotli-1.1.0-6.fc42.x86_64
libcap-2.73-2.fc42.x86_64
libcap-ng-0.8.5-4.fc42.x86_64
libcom_err-1.47.2-3.fc42.x86_64
libcurl-8.11.1-3.fc42.x86_64
libeconf-0.7.5-2.fc42.x86_64
libevent-2.1.12-15.fc42.x86_64
libfdisk-2.40.4-2.fc42.x86_64
libffi-3.4.6-5.fc42.x86_64
libgcc-15.0.1-0.5.fc42.x86_64
libgomp-15.0.1-0.5.fc42.x86_64
libidn2-2.3.7-3.fc42.x86_64
libmount-2.40.4-2.fc42.x86_64
libnghttp2-1.64.0-3.fc42.x86_64
libnsl2-2.0.1-3.fc42.x86_64
libpkgconf-2.3.0-2.fc42.x86_64
libpsl-0.21.5-5.fc42.x86_64
libpwquality-1.4.5-12.fc42.x86_64
libseccomp-2.5.5-2.fc41.x86_64
libselinux-3.8-1.fc42.x86_64
libsemanage-3.8-1.fc42.x86_64
libsepol-3.8-1.fc42.x86_64
libsmartcols-2.40.4-2.fc42.x86_64
libssh-0.11.1-4.fc42.x86_64
libssh-config-0.11.1-4.fc42.noarch
libstdc++-15.0.1-0.5.fc42.x86_64
libtasn1-4.19.0-11.fc42.x86_64
libtirpc-1.3.6-1.rc3.fc42.2.x86_64
libtool-ltdl-2.5.4-4.fc42.x86_64
libunistring-1.1-9.fc42.x86_64
libuuid-2.40.4-2.fc42.x86_64
libverto-0.3.2-10.fc42.x86_64
libxcrypt-4.4.38-4.fc42.x86_64
libxml2-2.12.9-2.fc42.x86_64
libzstd-1.5.6-3.fc42.x86_64
lua-libs-5.4.7-2.fc42.x86_64
lua-srpm-macros-1-15.fc42.noarch
lz4-libs-1.10.0-2.fc42.x86_64
mpfr-4.2.1-6.fc42.x86_64
ncurses-base-6.5-5.20250125.fc42.noarch
ncurses-libs-6.5-5.20250125.fc42.x86_64
ocaml-srpm-macros-10-4.fc42.noarch
openblas-srpm-macros-2-19.fc42.noarch
openldap-2.6.9-3.fc42.x86_64
openssl-libs-3.2.2-14.fc42.x86_64
p11-kit-0.25.5-5.fc42.x86_64
p11-kit-trust-0.25.5-5.fc42.x86_64
package-notes-srpm-macros-0.5-13.fc42.noarch
pam-1.7.0-4.fc42.x86_64
pam-libs-1.7.0-4.fc42.x86_64
patch-2.7.6-26.fc42.x86_64
pcre2-10.44-1.fc42.2.x86_64
pcre2-syntax-10.44-1.fc42.2.noarch
perl-srpm-macros-1-57.fc42.noarch
pkgconf-2.3.0-2.fc42.x86_64
pkgconf-m4-2.3.0-2.fc42.noarch
pkgconf-pkg-config-2.3.0-2.fc42.x86_64
popt-1.19-8.fc42.x86_64
publicsuffix-list-dafsa-20250116-1.fc42.noarch
pyproject-srpm-macros-1.16.4-2.fc42.noarch
python-srpm-macros-3.13-4.fc42.noarch
qt5-srpm-macros-5.15.15-1.fc42.noarch
qt6-srpm-macros-6.8.1-5.fc42.noarch
readline-8.2-12.fc42.x86_64
redhat-rpm-config-342-1.fc42.noarch
rpm-4.20.0-8.fc42.x86_64
rpm-build-4.20.0-8.fc42.x86_64
rpm-build-libs-4.20.0-8.fc42.x86_64
rpm-libs-4.20.0-8.fc42.x86_64
rpm-sequoia-1.7.0-4.fc42.x86_64
rust-srpm-macros-26.3-4.fc42.noarch
sed-4.9-4.fc42.x86_64
setup-2.15.0-10.fc42.noarch
shadow-utils-4.17.0-4.fc42.x86_64
sqlite-libs-3.47.2-2.fc42.x86_64
systemd-257.2-17.fc42.x86_64
systemd-libs-257.2-17.fc42.x86_64
systemd-pam-257.2-17.fc42.x86_64
systemd-rpm-macros-257.2-17.fc42.noarch
tar-1.35-5.fc42.x86_64
unzip-6.0-66.fc42.x86_64
util-linux-2.40.4-2.fc42.x86_64
util-linux-core-2.40.4-2.fc42.x86_64
which-2.22-2.fc42.x86_64
xxhash-libs-0.8.3-2.fc42.x86_64
xz-5.6.3-3.fc42.x86_64
xz-libs-5.6.3-3.fc42.x86_64
zig-srpm-macros-1-4.fc42.noarch
zip-3.0-43.fc42.x86_64
zlib-ng-compat-2.2.3-2.fc42.x86_64
zstd-1.5.6-3.fc42.x86_64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1737072000
Wrote: /builddir/build/SRPMS/mmseq-1.0.11-22.fc42.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_64-1738508284.648207/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-uvtf6f1v/mmseq/mmseq.spec) Config(child) 0 minutes 33 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-1.0.11-22.fc42.src.rpm)  Config(fedora-rawhide-x86_64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1738508284.648207/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1738508284.648207/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_64-1738508284.648207/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.20.0-1.fc42.x86_64
  rpm-sequoia-1.7.0-3.fc42.x86_64
  dnf5-5.2.8.1-2.fc42.x86_64
  dnf5-plugins-5.2.8.1-2.fc42.x86_64
Finish: chroot init
Start: build phase for mmseq-1.0.11-22.fc42.src.rpm
Start: build setup for mmseq-1.0.11-22.fc42.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1737072000
Wrote: /builddir/build/SRPMS/mmseq-1.0.11-22.fc42.src.rpm
Updating and loading repositories:
 fedora                                 100% | 698.0 KiB/s |  26.5 KiB |  00m00s
 Copr repository                        100% |  50.8 KiB/s |   1.5 KiB |  00m00s
Repositories loaded.
Package                      Arch   Version              Repository      Size
Installing:
 armadillo-devel             x86_64 12.8.1-6.fc42        fedora       7.3 MiB
 boost-devel                 x86_64 1.83.0-12.fc42       fedora     143.0 MiB
 flexiblas-devel             x86_64 3.4.4-7.fc42         fedora       4.8 MiB
 gcc-c++                     x86_64 15.0.1-0.5.fc42      fedora      41.3 MiB
 gsl-devel                   x86_64 2.8-1.fc42           copr_base    1.6 MiB
 htslib-devel                x86_64 1.15.1-8.fc42        fedora     411.0 KiB
 make                        x86_64 1:4.4.1-10.fc42      fedora       1.8 MiB
 perl-generators             noarch 1.16-7.fc42          fedora      21.8 KiB
 zlib-ng-compat-devel        x86_64 2.2.3-2.fc42         fedora     107.0 KiB
Installing dependencies:
 SuperLU                     x86_64 7.0.0-2.fc42         fedora     489.4 KiB
 SuperLU-devel               x86_64 7.0.0-2.fc42         fedora     103.5 KiB
 annobin-docs                noarch 12.87-1.fc42         fedora      98.6 KiB
 annobin-plugin-gcc          x86_64 12.87-1.fc42         fedora     991.8 KiB
 armadillo                   x86_64 12.8.1-6.fc42        fedora      82.6 KiB
 arpack                      x86_64 3.9.1-6.fc42         fedora     646.0 KiB
 arpack-devel                x86_64 3.9.1-6.fc42         fedora      69.1 KiB
 boost                       x86_64 1.83.0-12.fc42       fedora       1.3 KiB
 boost-atomic                x86_64 1.83.0-12.fc42       fedora      20.9 KiB
 boost-chrono                x86_64 1.83.0-12.fc42       fedora      37.5 KiB
 boost-container             x86_64 1.83.0-12.fc42       fedora      65.4 KiB
 boost-context               x86_64 1.83.0-12.fc42       fedora      12.4 KiB
 boost-contract              x86_64 1.83.0-12.fc42       fedora      99.1 KiB
 boost-coroutine             x86_64 1.83.0-12.fc42       fedora      21.1 KiB
 boost-date-time             x86_64 1.83.0-12.fc42       fedora      12.2 KiB
 boost-fiber                 x86_64 1.83.0-12.fc42       fedora      78.7 KiB
 boost-filesystem            x86_64 1.83.0-12.fc42       fedora     143.6 KiB
 boost-graph                 x86_64 1.83.0-12.fc42       fedora     350.7 KiB
 boost-iostreams             x86_64 1.83.0-12.fc42       fedora      90.6 KiB
 boost-json                  x86_64 1.83.0-12.fc42       fedora     333.1 KiB
 boost-locale                x86_64 1.83.0-12.fc42       fedora     613.8 KiB
 boost-log                   x86_64 1.83.0-12.fc42       fedora       1.5 MiB
 boost-math                  x86_64 1.83.0-12.fc42       fedora     642.6 KiB
 boost-nowide                x86_64 1.83.0-12.fc42       fedora      20.8 KiB
 boost-numpy3                x86_64 1.83.0-12.fc42       fedora      57.6 KiB
 boost-program-options       x86_64 1.83.0-12.fc42       fedora     276.7 KiB
 boost-python3               x86_64 1.83.0-12.fc42       fedora     254.4 KiB
 boost-random                x86_64 1.83.0-12.fc42       fedora      29.6 KiB
 boost-regex                 x86_64 1.83.0-12.fc42       fedora     287.3 KiB
 boost-serialization         x86_64 1.83.0-12.fc42       fedora     441.6 KiB
 boost-stacktrace            x86_64 1.83.0-12.fc42       fedora      55.8 KiB
 boost-system                x86_64 1.83.0-12.fc42       fedora      12.2 KiB
 boost-test                  x86_64 1.83.0-12.fc42       fedora     634.8 KiB
 boost-thread                x86_64 1.83.0-12.fc42       fedora     132.7 KiB
 boost-timer                 x86_64 1.83.0-12.fc42       fedora      21.0 KiB
 boost-type_erasure          x86_64 1.83.0-12.fc42       fedora      54.1 KiB
 boost-wave                  x86_64 1.83.0-12.fc42       fedora     856.2 KiB
 cmake-filesystem            x86_64 3.31.5-1.fc42        fedora       0.0   B
 cpp                         x86_64 15.0.1-0.5.fc42      fedora      38.0 MiB
 flexiblas                   x86_64 3.4.4-7.fc42         fedora      48.5 KiB
 flexiblas-netlib            x86_64 3.4.4-7.fc42         fedora      10.6 MiB
 flexiblas-netlib64          x86_64 3.4.4-7.fc42         fedora      10.7 MiB
 flexiblas-openblas-openmp   x86_64 3.4.4-7.fc42         fedora      43.2 KiB
 flexiblas-openblas-openmp64 x86_64 3.4.4-7.fc42         fedora      43.2 KiB
 gcc                         x86_64 15.0.1-0.5.fc42      fedora     111.0 MiB
 gcc-gfortran                x86_64 15.0.1-0.5.fc42      fedora      40.3 MiB
 gcc-plugin-annobin          x86_64 15.0.1-0.5.fc42      fedora      57.2 KiB
 glibc-devel                 x86_64 2.40.9000-35.fc42    fedora       2.3 MiB
 groff-base                  x86_64 1.23.0-8.fc42        fedora       3.9 MiB
 gsl                         x86_64 2.8-1.fc42           copr_base    3.5 MiB
 hdf5                        x86_64 1.14.5-2.fc42        fedora       7.1 MiB
 hdf5-devel                  x86_64 1.14.5-2.fc42        fedora       3.3 MiB
 htslib                      x86_64 1.15.1-8.fc42        fedora       1.1 MiB
 kernel-headers              x86_64 6.13.0-62.fc42       fedora       6.5 MiB
 libaec                      x86_64 1.1.3-2.fc42         fedora      97.9 KiB
 libaec-devel                x86_64 1.1.3-2.fc42         fedora      12.5 KiB
 libb2                       x86_64 0.98.1-13.fc42       fedora      46.1 KiB
 libgfortran                 x86_64 15.0.1-0.5.fc42      fedora       3.3 MiB
 libicu                      x86_64 76.1-4.fc42          fedora      36.3 MiB
 libicu-devel                x86_64 76.1-4.fc42          fedora       5.0 MiB
 libmpc                      x86_64 1.3.1-7.fc42         fedora     164.5 KiB
 libquadmath                 x86_64 15.0.1-0.5.fc42      fedora     317.9 KiB
 libquadmath-devel           x86_64 15.0.1-0.5.fc42      fedora      21.9 KiB
 libstdc++-devel             x86_64 15.0.1-0.5.fc42      fedora      15.9 MiB
 libxcrypt-devel             x86_64 4.4.38-4.fc42        fedora      30.8 KiB
 metis                       x86_64 5.1.0.3-7.fc42       fedora     980.1 KiB
 mpdecimal                   x86_64 2.5.1-17.fc42        fedora     200.8 KiB
 ncurses                     x86_64 6.5-5.20250125.fc42  fedora     608.1 KiB
 openblas                    x86_64 0.3.29-1.fc42        fedora     111.7 KiB
 openblas-openmp             x86_64 0.3.29-1.fc42        fedora      43.7 MiB
 openblas-openmp64           x86_64 0.3.29-1.fc42        fedora      43.9 MiB
 perl-AutoLoader             noarch 5.74-515.fc42        fedora      20.5 KiB
 perl-B                      x86_64 1.89-515.fc42        fedora     498.0 KiB
 perl-Carp                   noarch 1.54-512.fc42        fedora      46.6 KiB
 perl-Class-Struct           noarch 0.68-515.fc42        fedora      25.4 KiB
 perl-Data-Dumper            x86_64 2.189-513.fc42       fedora     115.6 KiB
 perl-Digest                 noarch 1.20-512.fc42        fedora      35.3 KiB
 perl-Digest-MD5             x86_64 2.59-6.fc42          fedora      59.7 KiB
 perl-DynaLoader             x86_64 1.56-515.fc42        fedora      32.1 KiB
 perl-Encode                 x86_64 4:3.21-512.fc42      fedora       4.7 MiB
 perl-Errno                  x86_64 1.38-515.fc42        fedora       8.3 KiB
 perl-Exporter               noarch 5.78-512.fc42        fedora      54.3 KiB
 perl-Fcntl                  x86_64 1.18-515.fc42        fedora      48.9 KiB
 perl-Fedora-VSP             noarch 0.001-36.fc42        fedora      39.7 KiB
 perl-File-Basename          noarch 2.86-515.fc42        fedora      14.0 KiB
 perl-File-Path              noarch 2.18-512.fc42        fedora      63.5 KiB
 perl-File-Temp              noarch 1:0.231.100-512.fc42 fedora     162.3 KiB
 perl-File-stat              noarch 1.14-515.fc42        fedora      12.5 KiB
 perl-FileHandle             noarch 2.05-515.fc42        fedora       9.3 KiB
 perl-Getopt-Long            noarch 1:2.58-3.fc42        fedora     144.5 KiB
 perl-Getopt-Std             noarch 1.14-515.fc42        fedora      11.2 KiB
 perl-HTTP-Tiny              noarch 0.090-2.fc42         fedora     154.4 KiB
 perl-IO                     x86_64 1.55-515.fc42        fedora     147.0 KiB
 perl-IO-Socket-IP           noarch 0.43-2.fc42          fedora     100.3 KiB
 perl-IO-Socket-SSL          noarch 2.089-2.fc42         fedora     703.3 KiB
 perl-IPC-Open3              noarch 1.22-515.fc42        fedora      22.5 KiB
 perl-MIME-Base32            noarch 1.303-23.fc42        fedora      30.7 KiB
 perl-MIME-Base64            x86_64 3.16-512.fc42        fedora      42.0 KiB
 perl-Net-SSLeay             x86_64 1.94-8.fc42          fedora       1.3 MiB
 perl-POSIX                  x86_64 2.20-515.fc42        fedora     231.0 KiB
 perl-PathTools              x86_64 3.91-513.fc42        fedora     180.0 KiB
 perl-Pod-Escapes            noarch 1:1.07-512.fc42      fedora      24.9 KiB
 perl-Pod-Perldoc            noarch 3.28.01-513.fc42     fedora     163.7 KiB
 perl-Pod-Simple             noarch 1:3.45-512.fc42      fedora     560.8 KiB
 perl-Pod-Usage              noarch 4:2.03-512.fc42      fedora      84.8 KiB
 perl-Scalar-List-Utils      x86_64 5:1.68-2.fc42        fedora     144.8 KiB
 perl-SelectSaver            noarch 1.02-515.fc42        fedora       2.2 KiB
 perl-Socket                 x86_64 4:2.038-512.fc42     fedora     119.9 KiB
 perl-Storable               x86_64 1:3.32-512.fc42      fedora     232.3 KiB
 perl-Symbol                 noarch 1.09-515.fc42        fedora       6.8 KiB
 perl-Term-ANSIColor         noarch 5.01-513.fc42        fedora      97.5 KiB
 perl-Term-Cap               noarch 1.18-512.fc42        fedora      29.3 KiB
 perl-Text-ParseWords        noarch 3.31-512.fc42        fedora      13.6 KiB
 perl-Text-Tabs+Wrap         noarch 2024.001-512.fc42    fedora      22.6 KiB
 perl-Time-Local             noarch 2:1.350-512.fc42     fedora      68.9 KiB
 perl-URI                    noarch 5.31-2.fc42          fedora     257.0 KiB
 perl-base                   noarch 2.27-515.fc42        fedora      12.5 KiB
 perl-constant               noarch 1.33-513.fc42        fedora      26.2 KiB
 perl-if                     noarch 0.61.000-515.fc42    fedora       5.8 KiB
 perl-interpreter            x86_64 4:5.40.1-515.fc42    fedora     118.1 KiB
 perl-libnet                 noarch 3.15-513.fc42        fedora     289.4 KiB
 perl-libs                   x86_64 4:5.40.1-515.fc42    fedora       9.8 MiB
 perl-locale                 noarch 1.12-515.fc42        fedora       6.5 KiB
 perl-macros                 noarch 4:5.40.1-515.fc42    fedora       5.5 KiB
 perl-mro                    x86_64 1.29-515.fc42        fedora      41.5 KiB
 perl-overload               noarch 1.37-515.fc42        fedora      71.5 KiB
 perl-overloading            noarch 0.02-515.fc42        fedora       4.8 KiB
 perl-parent                 noarch 1:0.244-2.fc42       fedora      10.3 KiB
 perl-podlators              noarch 1:6.0.2-3.fc42       fedora     317.5 KiB
 perl-vars                   noarch 1.05-515.fc42        fedora       3.9 KiB
 python-pip-wheel            noarch 24.3.1-2.fc42        fedora       1.2 MiB
 python3                     x86_64 3.13.1-3.fc42        fedora      27.6 KiB
 python3-libs                x86_64 3.13.1-3.fc42        fedora      39.9 MiB
 python3-numpy               x86_64 1:2.2.2-2.fc42       fedora      40.1 MiB
 python3-numpy-f2py          x86_64 1:2.2.2-2.fc42       fedora       2.0 MiB
 tzdata                      noarch 2024b-2.fc42         fedora       1.6 MiB

Transaction Summary:
 Installing:       145 packages

Total size of inbound packages is 172 MiB. Need to download 172 MiB.
After this operation, 705 MiB extra will be used (install 705 MiB, remove 0 B).
[  1/145] perl-generators-0:1.16-7.fc42 100% | 110.8 KiB/s |  16.3 KiB |  00m00s
[  2/145] make-1:4.4.1-10.fc42.x86_64   100% |   1.5 MiB/s | 587.0 KiB |  00m00s
[  3/145] flexiblas-devel-0:3.4.4-7.fc4 100% |   2.3 MiB/s | 121.9 KiB |  00m00s
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--------------------------------------------------------------------------------
[145/145] Total                         100% |  24.4 MiB/s | 172.1 MiB |  00m07s
Running transaction
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Warning: skipped OpenPGP checks for 2 packages from repository: copr_base
Complete!
Finish: build setup for mmseq-1.0.11-22.fc42.src.rpm
Start: rpmbuild mmseq-1.0.11-22.fc42.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1737072000
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.YWlgCc
+ 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
+ /usr/bin/rm -rf /builddir/build/BUILD/mmseq-1.0.11-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build/SPECPARTS
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.89Z18A
+ 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.wEwv0k
+ 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-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 -j2 '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;
      |       ^~~~~~~
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 -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 ‘_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++/15/algorithm:63,
                 from t2g_hits.cpp:27:
/usr/include/c++/15/bits/stl_algo.h:875:5: note: declared here
  875 |     unique(_ForwardIterator __first, _ForwardIterator __last)
      |     ^~~~~~
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
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 | }
      | ^
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: 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;
      |         ^~~~~~~
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
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 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
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: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;
      |        ^~~~~~~~~
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 fasta.o hitsio.o bam2hits.cpp -o ../bin/bam2hits -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
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: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")));
      |                                                        ^
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
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;
      |       ^~~~
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
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++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~
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
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++/15/algorithm:63,
                 from mmdiff.cpp:31:
/usr/include/c++/15/bits/stl_algo.h:4509:5: note: declared here
 4509 |     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++) {
      |                          ~~~~~~~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘initialise_streams’:
bms.cpp:1408:30: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1408 |   ofs = new ofstream[nstreams];
      |                              ^
/usr/include/c++/15/new:140:26: note: in a call to allocation function ‘operator new []’ declared here
  140 | _GLIBCXX_NODISCARD void* operator new[](std::size_t)
      |                          ^
/usr/bin/ld: /tmp/ccUGvJUs.ltrans1.ltrans.o: in function `main':
/builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/src/bam2hits.cpp:653:(.text.startup+0x528d): 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.z99O95
+ 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-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 -j2 --strict-build-id -m -i --build-id-seed 1.0.11-22.fc42 --unique-debug-suffix -1.0.11-22.fc42.x86_64 --unique-debug-src-base mmseq-1.0.11-22.fc42.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -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-1.0.11-22.fc42.x86_64
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
mangling shebang in /usr/bin/fastagrep.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/usage.sh from /bin/bash to #!/usr/bin/bash
mangling shebang in /usr/bin/filterGTF.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/testregexp.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/bin/ensembl_gtf_to_gff.pl from /usr/bin/env perl to #!/usr/bin/perl
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-determinism --brp -j2 /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
Reading /builddir/build/BUILD/mmseq-1.0.11-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.qY2UEl
+ 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-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-1.0.11-22.fc42.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.gH4lHf
+ 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 = 1.0.11-22.fc42 mmseq(x86-64) = 1.0.11-22.fc42
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-1.0.11-22.fc42.x86_64
Provides: mmseq-debugsource = 1.0.11-22.fc42 mmseq-debugsource(x86-64) = 1.0.11-22.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: mmseq-debuginfo-1.0.11-22.fc42.x86_64
Provides: debuginfo(build-id) = 075b27847ed08ffa4182c8eb96b71fc400dceecb debuginfo(build-id) = 30b3911df1f4d4f0eccce9ab2f87e6579552a7f9 debuginfo(build-id) = 4fd88ee8335744c590bea9f2b40e1114c7f5ff88 debuginfo(build-id) = a25b3d75990a80689eceb07b075dfe937ad9e405 debuginfo(build-id) = c42a135eb3ad0938d21811a3ae71bcea854cb02b debuginfo(build-id) = c544b77d888657f49b3808b5f94630d51797a3e1 debuginfo(build-id) = f46db7331e8cc7bac94834261714ddfbf55f4264 debuginfo(build-id) = f81a0a3b0851d7f081caa40385eed65b26a407b8 mmseq-debuginfo = 1.0.11-22.fc42 mmseq-debuginfo(x86-64) = 1.0.11-22.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: mmseq-debugsource(x86-64) = 1.0.11-22.fc42
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT
Wrote: /builddir/build/RPMS/mmseq-1.0.11-22.fc42.x86_64.rpm
Wrote: /builddir/build/RPMS/mmseq-debugsource-1.0.11-22.fc42.x86_64.rpm
Wrote: /builddir/build/RPMS/mmseq-debuginfo-1.0.11-22.fc42.x86_64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.subCfW
+ 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-1.0.11-22.fc42.src.rpm
Finish: build phase for mmseq-1.0.11-22.fc42.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1738508284.648207/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-1.0.11-22.fc42.src.rpm) Config(child) 1 minutes 43 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-debugsource",
            "epoch": null,
            "version": "1.0.11",
            "release": "22.fc42",
            "arch": "x86_64"
        },
        {
            "name": "mmseq",
            "epoch": null,
            "version": "1.0.11",
            "release": "22.fc42",
            "arch": "src"
        },
        {
            "name": "mmseq",
            "epoch": null,
            "version": "1.0.11",
            "release": "22.fc42",
            "arch": "x86_64"
        },
        {
            "name": "mmseq-debuginfo",
            "epoch": null,
            "version": "1.0.11",
            "release": "22.fc42",
            "arch": "x86_64"
        }
    ]
}
RPMResults finished