Warning: Permanently added '3.85.12.55' (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/6745622-fedora-rawhide-aarch64 --chroot fedora-rawhide-aarch64


Version: 0.70
PID: 6045
Logging PID: 6046
Task:
{'appstream': False,
 'background': True,
 'build_id': 6745622,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-aarch64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '2ed9d1e86a2a9ad4b2b3dea57cbe20a8b80d3205',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ppalka/boost-1.83-all-arches/mmseq',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'mmseq',
 'package_version': '1.0.11-16',
 'project_dirname': 'boost-1.83-all-arches',
 'project_name': 'boost-1.83-all-arches',
 'project_owner': 'ppalka',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ppalka/boost-1.83-all-arches/fedora-rawhide-aarch64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'ppalka/boost-1.83-all-arches--ppalka',
 'source_json': {},
 'source_type': None,
 'submitter': 'ppalka',
 'tags': [],
 'task_id': '6745622-fedora-rawhide-aarch64',
 'timeout': 115200,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ppalka/boost-1.83-all-arches/mmseq /var/lib/copr-rpmbuild/workspace/workdir-6klsy1ke/mmseq --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ppalka/boost-1.83-all-arches/mmseq', '/var/lib/copr-rpmbuild/workspace/workdir-6klsy1ke/mmseq', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-6klsy1ke/mmseq'...

Running: git checkout 2ed9d1e86a2a9ad4b2b3dea57cbe20a8b80d3205 --

cmd: ['git', 'checkout', '2ed9d1e86a2a9ad4b2b3dea57cbe20a8b80d3205', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-6klsy1ke/mmseq
rc: 0
stdout: 
stderr: Note: switching to '2ed9d1e86a2a9ad4b2b3dea57cbe20a8b80d3205'.

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 2ed9d1e automatic import of mmseq

Running: copr-distgit-client sources

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-6klsy1ke/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/ppalka/boost-1.83-all-arches/mmseq/1.0.11.zip/md5/c727916d339d7a2111523800b621ce2b/1.0.11.zip
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 2781k  100 2781k    0     0  27.4M      0 --:--:-- --:--:-- --:--:-- 27.7M
INFO: Reading stdout from command: md5sum 1.0.11.zip

Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-6klsy1ke/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-6klsy1ke/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1702411319.400365 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.2 starting (python version = 3.11.3, NVR = mock-5.2-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-6klsy1ke/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-6klsy1ke/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1702411319.400365 -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-6klsy1ke/mmseq/mmseq.spec)  Config(fedora-rawhide-aarch64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.2
INFO: Mock Version: 5.2
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1702411319.400365/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide
INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide
INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1702411319.400365/root
INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture
INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount
INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/5694bb9f3b561a16b30673b766681d672f702ac440aa31b5636b944d5fff154f/merged
INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/5694bb9f3b561a16b30673b766681d672f702ac440aa31b5636b944d5fff154f/merged) with podman image umount
INFO: Package manager dnf detected and used (fallback)
INFO: Bootstrap image not marked ready
Start(bootstrap): installing dnf tooling
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  31 MB/s | 1.7 MB     00:00    
fedora                                           42 MB/s |  69 MB     00:01    
Package python3-dnf-4.18.2-1.fc40.noarch is already installed.
Dependencies resolved.
================================================================================
 Package                      Arch        Version              Repository  Size
================================================================================
Installing:
 python3-dnf-plugins-core     noarch      4.4.4-1.fc40         fedora     317 k
Installing dependencies:
 dbus-libs                    aarch64     1:1.14.10-1.fc40     fedora     156 k
 python3-dateutil             noarch      1:2.8.2-11.fc40      fedora     356 k
 python3-dbus                 aarch64     1.3.2-4.fc39         fedora     157 k
 python3-distro               noarch      1.8.0-6.fc39         fedora      49 k
 python3-six                  noarch      1.16.0-12.fc39       fedora      41 k
 python3-systemd              aarch64     235-5.fc39           fedora     107 k

Transaction Summary
================================================================================
Install  7 Packages

Total download size: 1.2 M
Installed size: 4.7 M
Downloading Packages:
(1/7): dbus-libs-1.14.10-1.fc40.aarch64.rpm     7.2 MB/s | 156 kB     00:00    
(2/7): python3-dbus-1.3.2-4.fc39.aarch64.rpm    6.8 MB/s | 157 kB     00:00    
(3/7): python3-distro-1.8.0-6.fc39.noarch.rpm    22 MB/s |  49 kB     00:00    
(4/7): python3-dnf-plugins-core-4.4.4-1.fc40.no 109 MB/s | 317 kB     00:00    
(5/7): python3-six-1.16.0-12.fc39.noarch.rpm     14 MB/s |  41 kB     00:00    
(6/7): python3-systemd-235-5.fc39.aarch64.rpm    53 MB/s | 107 kB     00:00    
(7/7): python3-dateutil-2.8.2-11.fc40.noarch.rp  12 MB/s | 356 kB     00:00    
--------------------------------------------------------------------------------
Total                                            15 MB/s | 1.2 MB     00:00     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
  Installing       : python3-systemd-235-5.fc39.aarch64                     1/7 
  Installing       : python3-six-1.16.0-12.fc39.noarch                      2/7 
  Installing       : python3-dateutil-1:2.8.2-11.fc40.noarch                3/7 
  Installing       : python3-distro-1.8.0-6.fc39.noarch                     4/7 
  Installing       : dbus-libs-1:1.14.10-1.fc40.aarch64                     5/7 
  Installing       : python3-dbus-1.3.2-4.fc39.aarch64                      6/7 
  Installing       : python3-dnf-plugins-core-4.4.4-1.fc40.noarch           7/7 
  Running scriptlet: python3-dnf-plugins-core-4.4.4-1.fc40.noarch           7/7 

Installed:
  dbus-libs-1:1.14.10-1.fc40.aarch64                                            
  python3-dateutil-1:2.8.2-11.fc40.noarch                                       
  python3-dbus-1.3.2-4.fc39.aarch64                                             
  python3-distro-1.8.0-6.fc39.noarch                                            
  python3-dnf-plugins-core-4.4.4-1.fc40.noarch                                  
  python3-six-1.16.0-12.fc39.noarch                                             
  python3-systemd-235-5.fc39.aarch64                                            

Complete!
Finish(bootstrap): installing dnf tooling
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-1702411319.400365/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf detected and used (direct choice)
Start: installing minimal buildroot with dnf
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  27 MB/s | 1.7 MB     00:00    
fedora                                           49 MB/s |  69 MB     00:01    
Last metadata expiration check: 0:00:01 ago on Tue Dec 12 20:02:31 2023.
Dependencies resolved.
================================================================================
 Package                       Arch    Version                     Repo    Size
================================================================================
Installing group/module packages:
 bash                          aarch64 5.2.21-2.fc40               fedora 1.8 M
 bzip2                         aarch64 1.0.8-16.fc39               fedora  52 k
 coreutils                     aarch64 9.4-1.fc40                  fedora 1.2 M
 cpio                          aarch64 2.14-5.fc40                 fedora 277 k
 diffutils                     aarch64 3.10-3.fc39                 fedora 396 k
 fedora-release-common         noarch  40-0.20                     fedora  20 k
 findutils                     aarch64 1:4.9.0-6.fc40              fedora 495 k
 gawk                          aarch64 5.2.2-2.fc39                fedora 1.1 M
 glibc-minimal-langpack        aarch64 2.38.9000-26.fc40           fedora  85 k
 grep                          aarch64 3.11-5.fc40                 fedora 296 k
 gzip                          aarch64 1.12-6.fc39                 fedora 164 k
 info                          aarch64 7.1-1.fc40                  fedora 183 k
 patch                         aarch64 2.7.6-22.fc39               fedora 123 k
 redhat-rpm-config             noarch  271-1.fc40                  fedora  81 k
 rpm-build                     aarch64 4.19.0-3.fc40               fedora  80 k
 sed                           aarch64 4.8-14.fc39                 fedora 304 k
 shadow-utils                  aarch64 2:4.14.0-2.fc40             fedora 1.3 M
 tar                           aarch64 2:1.35-2.fc40               fedora 854 k
 unzip                         aarch64 6.0-62.fc39                 fedora 183 k
 util-linux                    aarch64 2.39.2-1.fc40               fedora 1.2 M
 which                         aarch64 2.21-40.fc39                fedora  42 k
 xz                            aarch64 5.4.5-1.fc40                fedora 557 k
Installing dependencies:
 alternatives                  aarch64 1.25-1.fc39                 fedora  38 k
 ansible-srpm-macros           noarch  1-11.fc39                   fedora  21 k
 audit-libs                    aarch64 3.1.2-5.fc40                fedora 118 k
 authselect                    aarch64 1.4.3-1.fc40                fedora 149 k
 authselect-libs               aarch64 1.4.3-1.fc40                fedora 249 k
 basesystem                    noarch  11-18.fc39                  fedora 7.2 k
 binutils                      aarch64 2.41-16.fc40                fedora 6.7 M
 binutils-gold                 aarch64 2.41-16.fc40                fedora 945 k
 bzip2-libs                    aarch64 1.0.8-16.fc39               fedora  43 k
 ca-certificates               noarch  2023.2.62_v7.0.401-4.fc40   fedora 863 k
 coreutils-common              aarch64 9.4-1.fc40                  fedora 2.1 M
 cracklib                      aarch64 2.9.11-2.fc39               fedora  94 k
 crypto-policies               noarch  20231204-1.git1e3a2e4.fc40  fedora 100 k
 curl                          aarch64 8.5.0-1.fc40                fedora 368 k
 cyrus-sasl-lib                aarch64 2.1.28-11.fc39              fedora 781 k
 debugedit                     aarch64 5.0-12.fc40                 fedora  78 k
 dwz                           aarch64 0.15-3.fc39                 fedora 136 k
 ed                            aarch64 1.19-4.fc39                 fedora  78 k
 efi-srpm-macros               noarch  5-9.fc39                    fedora  22 k
 elfutils                      aarch64 0.190-4.fc40                fedora 552 k
 elfutils-debuginfod-client    aarch64 0.190-4.fc40                fedora  37 k
 elfutils-default-yama-scope   noarch  0.190-4.fc40                fedora  13 k
 elfutils-libelf               aarch64 0.190-4.fc40                fedora 194 k
 elfutils-libs                 aarch64 0.190-4.fc40                fedora 259 k
 fedora-gpg-keys               noarch  40-0.2                      fedora 130 k
 fedora-release                noarch  40-0.20                     fedora 9.3 k
 fedora-release-identity-basic noarch  40-0.20                     fedora  10 k
 fedora-repos                  noarch  40-0.2                      fedora 9.3 k
 fedora-repos-rawhide          noarch  40-0.2                      fedora 8.9 k
 file                          aarch64 5.45-1.fc40                 fedora  49 k
 file-libs                     aarch64 5.45-1.fc40                 fedora 761 k
 filesystem                    aarch64 3.18-6.fc39                 fedora 1.1 M
 fonts-srpm-macros             noarch  1:2.0.5-12.fc39             fedora  26 k
 forge-srpm-macros             noarch  0.2.0-1.fc40                fedora  18 k
 fpc-srpm-macros               noarch  1.3-8.fc39                  fedora 7.4 k
 gdb-minimal                   aarch64 14.1-1.fc40                 fedora 3.9 M
 gdbm                          aarch64 1:1.23-4.fc39               fedora 153 k
 gdbm-libs                     aarch64 1:1.23-4.fc39               fedora  56 k
 ghc-srpm-macros               noarch  1.6.1-3.fc40                fedora 8.1 k
 glibc                         aarch64 2.38.9000-26.fc40           fedora 1.8 M
 glibc-common                  aarch64 2.38.9000-26.fc40           fedora 363 k
 glibc-gconv-extra             aarch64 2.38.9000-26.fc40           fedora 2.0 M
 gmp                           aarch64 1:6.2.1-5.fc39              fedora 266 k
 gnat-srpm-macros              noarch  6-3.fc39                    fedora 8.8 k
 go-srpm-macros                noarch  3.3.1-1.fc40                fedora  28 k
 jansson                       aarch64 2.13.1-7.fc39               fedora  46 k
 kernel-srpm-macros            noarch  1.0-20.fc39                 fedora  10 k
 keyutils-libs                 aarch64 1.6.1-7.fc39                fedora  31 k
 krb5-libs                     aarch64 1.21.2-2.fc40               fedora 769 k
 libacl                        aarch64 2.3.1-11.fc40               fedora  24 k
 libarchive                    aarch64 3.7.2-1.fc40                fedora 402 k
 libattr                       aarch64 2.5.1-9.fc40                fedora  18 k
 libblkid                      aarch64 2.39.2-1.fc40               fedora 115 k
 libbrotli                     aarch64 1.1.0-1.fc40                fedora 344 k
 libcap                        aarch64 2.69-1.fc40                 fedora  84 k
 libcap-ng                     aarch64 0.8.3-8.fc40                fedora  32 k
 libcom_err                    aarch64 1.47.0-2.fc39               fedora  26 k
 libcurl                       aarch64 8.5.0-1.fc40                fedora 338 k
 libeconf                      aarch64 0.5.2-1.fc40                fedora  30 k
 libevent                      aarch64 2.1.12-9.fc39               fedora 254 k
 libfdisk                      aarch64 2.39.2-1.fc40               fedora 158 k
 libffi                        aarch64 3.4.4-4.fc39                fedora  38 k
 libgcc                        aarch64 13.2.1-6.fc40               fedora  97 k
 libgomp                       aarch64 13.2.1-6.fc40               fedora 313 k
 libidn2                       aarch64 2.3.4-3.fc39                fedora 118 k
 libmount                      aarch64 2.39.2-1.fc40               fedora 153 k
 libnghttp2                    aarch64 1.58.0-1.fc40               fedora  76 k
 libnsl2                       aarch64 2.0.0-6.fc39                fedora  30 k
 libpkgconf                    aarch64 1.9.5-2.fc39                fedora  38 k
 libpsl                        aarch64 0.21.2-4.fc39               fedora  63 k
 libpwquality                  aarch64 1.4.5-6.fc39                fedora 120 k
 libselinux                    aarch64 3.6-0.rc2.1.fc40            fedora  87 k
 libsemanage                   aarch64 3.6-0.rc2.1.fc40            fedora 114 k
 libsepol                      aarch64 3.6-0.rc2.1.fc40            fedora 324 k
 libsigsegv                    aarch64 2.14-5.fc39                 fedora  27 k
 libsmartcols                  aarch64 2.39.2-1.fc40               fedora  65 k
 libssh                        aarch64 0.10.5-2.fc39               fedora 212 k
 libssh-config                 noarch  0.10.5-2.fc39               fedora 9.2 k
 libstdc++                     aarch64 13.2.1-6.fc40               fedora 814 k
 libtasn1                      aarch64 4.19.0-3.fc39               fedora  73 k
 libtirpc                      aarch64 1.3.4-0.fc40                fedora  95 k
 libunistring                  aarch64 1.1-5.fc40                  fedora 540 k
 libutempter                   aarch64 1.2.1-10.fc39               fedora  27 k
 libuuid                       aarch64 2.39.2-1.fc40               fedora  28 k
 libverto                      aarch64 0.3.2-6.fc39                fedora  21 k
 libxcrypt                     aarch64 4.4.36-2.fc39               fedora 123 k
 libxml2                       aarch64 2.12.2-2.fc40               fedora 682 k
 libzstd                       aarch64 1.5.5-4.fc39                fedora 280 k
 lua-libs                      aarch64 5.4.6-3.fc39                fedora 131 k
 lua-srpm-macros               noarch  1-9.fc39                    fedora 8.6 k
 lz4-libs                      aarch64 1.9.4-4.fc39                fedora  68 k
 mpfr                          aarch64 4.2.1-1.fc40                fedora 320 k
 ncurses-base                  noarch  6.4-8.20231001.fc40         fedora  88 k
 ncurses-libs                  aarch64 6.4-8.20231001.fc40         fedora 328 k
 ocaml-srpm-macros             noarch  9-1.fc40                    fedora 9.0 k
 openblas-srpm-macros          noarch  2-14.fc39                   fedora 7.5 k
 openldap                      aarch64 2.6.6-1.fc39                fedora 251 k
 openssl-libs                  aarch64 1:3.1.4-1.fc40              fedora 2.0 M
 p11-kit                       aarch64 0.25.3-1.fc40               fedora 495 k
 p11-kit-trust                 aarch64 0.25.3-1.fc40               fedora 141 k
 package-notes-srpm-macros     noarch  0.5-9.fc39                  fedora  11 k
 pam                           aarch64 1.5.3-8.fc40                fedora 557 k
 pam-libs                      aarch64 1.5.3-8.fc40                fedora  57 k
 pcre2                         aarch64 10.42-2.fc40                fedora 219 k
 pcre2-syntax                  noarch  10.42-2.fc40                fedora 143 k
 perl-srpm-macros              noarch  1-51.fc39                   fedora 8.0 k
 pkgconf                       aarch64 1.9.5-2.fc39                fedora  42 k
 pkgconf-m4                    noarch  1.9.5-2.fc39                fedora  14 k
 pkgconf-pkg-config            aarch64 1.9.5-2.fc39                fedora 9.6 k
 popt                          aarch64 1.19-3.fc39                 fedora  66 k
 publicsuffix-list-dafsa       noarch  20230812-1.fc40             fedora  57 k
 pyproject-srpm-macros         noarch  1.10.0-1.fc40               fedora  14 k
 python-srpm-macros            noarch  3.12-5.fc40                 fedora  25 k
 qt5-srpm-macros               noarch  5.15.11-1.fc40              fedora 8.3 k
 qt6-srpm-macros               noarch  6.6.1-1.fc40                fedora 8.6 k
 readline                      aarch64 8.2-4.fc39                  fedora 211 k
 rpm                           aarch64 4.19.0-3.fc40               fedora 537 k
 rpm-build-libs                aarch64 4.19.0-3.fc40               fedora  92 k
 rpm-libs                      aarch64 4.19.0-3.fc40               fedora 306 k
 rpm-sequoia                   aarch64 1.5.0-2.fc40                fedora 839 k
 rust-srpm-macros              noarch  25.2-2.fc40                 fedora  13 k
 setup                         noarch  2.14.5-1.fc40               fedora 155 k
 sqlite-libs                   aarch64 3.44.2-1.fc40               fedora 685 k
 systemd-libs                  aarch64 255-1.fc40                  fedora 680 k
 util-linux-core               aarch64 2.39.2-1.fc40               fedora 490 k
 xxhash-libs                   aarch64 0.8.2-1.fc39                fedora  35 k
 xz-libs                       aarch64 5.4.5-1.fc40                fedora 107 k
 zip                           aarch64 3.0-39.fc40                 fedora 262 k
 zlib                          aarch64 1.2.13-5.fc40               fedora  93 k
 zstd                          aarch64 1.5.5-4.fc39                fedora 446 k
Installing Groups:
 Buildsystem building group                                                    

Transaction Summary
================================================================================
Install  152 Packages

Total download size: 52 M
Installed size: 303 M
Downloading Packages:
(1/152): alternatives-1.25-1.fc39.aarch64.rpm   1.9 MB/s |  38 kB     00:00    
(2/152): audit-libs-3.1.2-5.fc40.aarch64.rpm    5.6 MB/s | 118 kB     00:00    
(3/152): ansible-srpm-macros-1-11.fc39.noarch.r 972 kB/s |  21 kB     00:00    
(4/152): basesystem-11-18.fc39.noarch.rpm       2.4 MB/s | 7.2 kB     00:00    
(5/152): authselect-1.4.3-1.fc40.aarch64.rpm     18 MB/s | 149 kB     00:00    
(6/152): authselect-libs-1.4.3-1.fc40.aarch64.r  21 MB/s | 249 kB     00:00    
(7/152): bash-5.2.21-2.fc40.aarch64.rpm          39 MB/s | 1.8 MB     00:00    
(8/152): bzip2-1.0.8-16.fc39.aarch64.rpm         13 MB/s |  52 kB     00:00    
(9/152): binutils-gold-2.41-16.fc40.aarch64.rpm  20 MB/s | 945 kB     00:00    
(10/152): bzip2-libs-1.0.8-16.fc39.aarch64.rpm   10 MB/s |  43 kB     00:00    
(11/152): ca-certificates-2023.2.62_v7.0.401-4.  39 MB/s | 863 kB     00:00    
(12/152): coreutils-9.4-1.fc40.aarch64.rpm       19 MB/s | 1.2 MB     00:00    
(13/152): coreutils-common-9.4-1.fc40.aarch64.r  40 MB/s | 2.1 MB     00:00    
(14/152): cpio-2.14-5.fc40.aarch64.rpm           17 MB/s | 277 kB     00:00    
(15/152): crypto-policies-20231204-1.git1e3a2e4  27 MB/s | 100 kB     00:00    
(16/152): cracklib-2.9.11-2.fc39.aarch64.rpm     14 MB/s |  94 kB     00:00    
(17/152): curl-8.5.0-1.fc40.aarch64.rpm          19 MB/s | 368 kB     00:00    
(18/152): cyrus-sasl-lib-2.1.28-11.fc39.aarch64  43 MB/s | 781 kB     00:00    
(19/152): debugedit-5.0-12.fc40.aarch64.rpm      15 MB/s |  78 kB     00:00    
(20/152): dwz-0.15-3.fc39.aarch64.rpm            27 MB/s | 136 kB     00:00    
(21/152): diffutils-3.10-3.fc39.aarch64.rpm      20 MB/s | 396 kB     00:00    
(22/152): efi-srpm-macros-5-9.fc39.noarch.rpm   7.9 MB/s |  22 kB     00:00    
(23/152): binutils-2.41-16.fc40.aarch64.rpm      35 MB/s | 6.7 MB     00:00    
(24/152): elfutils-0.190-4.fc40.aarch64.rpm      28 MB/s | 552 kB     00:00    
(25/152): elfutils-default-yama-scope-0.190-4.f 5.2 MB/s |  13 kB     00:00    
(26/152): elfutils-debuginfod-client-0.190-4.fc 9.2 MB/s |  37 kB     00:00    
(27/152): ed-1.19-4.fc39.aarch64.rpm            1.8 MB/s |  78 kB     00:00    
(28/152): fedora-gpg-keys-40-0.2.noarch.rpm      12 MB/s | 130 kB     00:00    
(29/152): elfutils-libs-0.190-4.fc40.aarch64.rp  14 MB/s | 259 kB     00:00    
(30/152): fedora-release-40-0.20.noarch.rpm     3.3 MB/s | 9.3 kB     00:00    
(31/152): fedora-release-common-40-0.20.noarch. 6.3 MB/s |  20 kB     00:00    
(32/152): fedora-release-identity-basic-40-0.20 4.1 MB/s |  10 kB     00:00    
(33/152): fedora-repos-40-0.2.noarch.rpm        3.1 MB/s | 9.3 kB     00:00    
(34/152): fedora-repos-rawhide-40-0.2.noarch.rp 1.8 MB/s | 8.9 kB     00:00    
(35/152): file-5.45-1.fc40.aarch64.rpm           13 MB/s |  49 kB     00:00    
(36/152): filesystem-3.18-6.fc39.aarch64.rpm     48 MB/s | 1.1 MB     00:00    
(37/152): file-libs-5.45-1.fc40.aarch64.rpm      20 MB/s | 761 kB     00:00    
(38/152): findutils-4.9.0-6.fc40.aarch64.rpm     36 MB/s | 495 kB     00:00    
(39/152): fonts-srpm-macros-2.0.5-12.fc39.noarc 6.2 MB/s |  26 kB     00:00    
(40/152): forge-srpm-macros-0.2.0-1.fc40.noarch 5.0 MB/s |  18 kB     00:00    
(41/152): fpc-srpm-macros-1.3-8.fc39.noarch.rpm 2.1 MB/s | 7.4 kB     00:00    
(42/152): gawk-5.2.2-2.fc39.aarch64.rpm          34 MB/s | 1.1 MB     00:00    
(43/152): gdbm-1.23-4.fc39.aarch64.rpm           17 MB/s | 153 kB     00:00    
(44/152): gdbm-libs-1.23-4.fc39.aarch64.rpm      11 MB/s |  56 kB     00:00    
(45/152): ghc-srpm-macros-1.6.1-3.fc40.noarch.r 3.8 MB/s | 8.1 kB     00:00    
(46/152): gdb-minimal-14.1-1.fc40.aarch64.rpm    36 MB/s | 3.9 MB     00:00    
(47/152): glibc-common-2.38.9000-26.fc40.aarch6  31 MB/s | 363 kB     00:00    
(48/152): elfutils-libelf-0.190-4.fc40.aarch64. 938 kB/s | 194 kB     00:00    
(49/152): glibc-minimal-langpack-2.38.9000-26.f  11 MB/s |  85 kB     00:00    
(50/152): gmp-6.2.1-5.fc39.aarch64.rpm           37 MB/s | 266 kB     00:00    
(51/152): gnat-srpm-macros-6-3.fc39.noarch.rpm  1.0 MB/s | 8.8 kB     00:00    
(52/152): go-srpm-macros-3.3.1-1.fc40.noarch.rp 1.8 MB/s |  28 kB     00:00    
(53/152): grep-3.11-5.fc40.aarch64.rpm           34 MB/s | 296 kB     00:00    
(54/152): gzip-1.12-6.fc39.aarch64.rpm          7.8 MB/s | 164 kB     00:00    
(55/152): glibc-gconv-extra-2.38.9000-26.fc40.a  24 MB/s | 2.0 MB     00:00    
(56/152): jansson-2.13.1-7.fc39.aarch64.rpm      14 MB/s |  46 kB     00:00    
(57/152): kernel-srpm-macros-1.0-20.fc39.noarch 3.5 MB/s |  10 kB     00:00    
(58/152): info-7.1-1.fc40.aarch64.rpm            15 MB/s | 183 kB     00:00    
(59/152): keyutils-libs-1.6.1-7.fc39.aarch64.rp 7.6 MB/s |  31 kB     00:00    
(60/152): libacl-2.3.1-11.fc40.aarch64.rpm      8.5 MB/s |  24 kB     00:00    
(61/152): libarchive-3.7.2-1.fc40.aarch64.rpm    31 MB/s | 402 kB     00:00    
(62/152): krb5-libs-1.21.2-2.fc40.aarch64.rpm    39 MB/s | 769 kB     00:00    
(63/152): libattr-2.5.1-9.fc40.aarch64.rpm      6.2 MB/s |  18 kB     00:00    
(64/152): libbrotli-1.1.0-1.fc40.aarch64.rpm     38 MB/s | 344 kB     00:00    
(65/152): libcap-2.69-1.fc40.aarch64.rpm         21 MB/s |  84 kB     00:00    
(66/152): libcap-ng-0.8.3-8.fc40.aarch64.rpm    2.7 MB/s |  32 kB     00:00    
(67/152): libblkid-2.39.2-1.fc40.aarch64.rpm    2.8 MB/s | 115 kB     00:00    
(68/152): libcom_err-1.47.0-2.fc39.aarch64.rpm  1.4 MB/s |  26 kB     00:00    
(69/152): libeconf-0.5.2-1.fc40.aarch64.rpm     4.7 MB/s |  30 kB     00:00    
(70/152): libcurl-8.5.0-1.fc40.aarch64.rpm       18 MB/s | 338 kB     00:00    
(71/152): libfdisk-2.39.2-1.fc40.aarch64.rpm     28 MB/s | 158 kB     00:00    
(72/152): libevent-2.1.12-9.fc39.aarch64.rpm     19 MB/s | 254 kB     00:00    
(73/152): libffi-3.4.4-4.fc39.aarch64.rpm       8.6 MB/s |  38 kB     00:00    
(74/152): libgcc-13.2.1-6.fc40.aarch64.rpm       15 MB/s |  97 kB     00:00    
(75/152): libidn2-2.3.4-3.fc39.aarch64.rpm       21 MB/s | 118 kB     00:00    
(76/152): libgomp-13.2.1-6.fc40.aarch64.rpm      32 MB/s | 313 kB     00:00    
(77/152): libnghttp2-1.58.0-1.fc40.aarch64.rpm   16 MB/s |  76 kB     00:00    
(78/152): libmount-2.39.2-1.fc40.aarch64.rpm     24 MB/s | 153 kB     00:00    
(79/152): libnsl2-2.0.0-6.fc39.aarch64.rpm      7.6 MB/s |  30 kB     00:00    
(80/152): libpkgconf-1.9.5-2.fc39.aarch64.rpm    11 MB/s |  38 kB     00:00    
(81/152): libpwquality-1.4.5-6.fc39.aarch64.rpm  18 MB/s | 120 kB     00:00    
(82/152): libpsl-0.21.2-4.fc39.aarch64.rpm      2.6 MB/s |  63 kB     00:00    
(83/152): libsemanage-3.6-0.rc2.1.fc40.aarch64.  28 MB/s | 114 kB     00:00    
(84/152): libselinux-3.6-0.rc2.1.fc40.aarch64.r 2.0 MB/s |  87 kB     00:00    
(85/152): libsigsegv-2.14-5.fc39.aarch64.rpm    9.6 MB/s |  27 kB     00:00    
(86/152): libsmartcols-2.39.2-1.fc40.aarch64.rp  10 MB/s |  65 kB     00:00    
(87/152): libsepol-3.6-0.rc2.1.fc40.aarch64.rpm 9.9 MB/s | 324 kB     00:00    
(88/152): libssh-config-0.10.5-2.fc39.noarch.rp 1.9 MB/s | 9.2 kB     00:00    
(89/152): libssh-0.10.5-2.fc39.aarch64.rpm       21 MB/s | 212 kB     00:00    
(90/152): glibc-2.38.9000-26.fc40.aarch64.rpm   5.0 MB/s | 1.8 MB     00:00    
(91/152): libtasn1-4.19.0-3.fc39.aarch64.rpm    5.9 MB/s |  73 kB     00:00    
(92/152): libtirpc-1.3.4-0.fc40.aarch64.rpm      17 MB/s |  95 kB     00:00    
(93/152): libutempter-1.2.1-10.fc39.aarch64.rpm 4.5 MB/s |  27 kB     00:00    
(94/152): libstdc++-13.2.1-6.fc40.aarch64.rpm    29 MB/s | 814 kB     00:00    
(95/152): libuuid-2.39.2-1.fc40.aarch64.rpm     4.7 MB/s |  28 kB     00:00    
(96/152): libverto-0.3.2-6.fc39.aarch64.rpm     5.4 MB/s |  21 kB     00:00    
(97/152): libxcrypt-4.4.36-2.fc39.aarch64.rpm    28 MB/s | 123 kB     00:00    
(98/152): libunistring-1.1-5.fc40.aarch64.rpm    29 MB/s | 540 kB     00:00    
(99/152): lua-libs-5.4.6-3.fc39.aarch64.rpm      22 MB/s | 131 kB     00:00    
(100/152): libzstd-1.5.5-4.fc39.aarch64.rpm      37 MB/s | 280 kB     00:00    
(101/152): lua-srpm-macros-1-9.fc39.noarch.rpm  5.3 MB/s | 8.6 kB     00:00    
(102/152): lz4-libs-1.9.4-4.fc39.aarch64.rpm     16 MB/s |  68 kB     00:00    
(103/152): libxml2-2.12.2-2.fc40.aarch64.rpm     31 MB/s | 682 kB     00:00    
(104/152): ncurses-base-6.4-8.20231001.fc40.noa  11 MB/s |  88 kB     00:00    
(105/152): ocaml-srpm-macros-9-1.fc40.noarch.rp 3.9 MB/s | 9.0 kB     00:00    
(106/152): mpfr-4.2.1-1.fc40.aarch64.rpm         21 MB/s | 320 kB     00:00    
(107/152): openblas-srpm-macros-2-14.fc39.noarc 2.4 MB/s | 7.5 kB     00:00    
(108/152): ncurses-libs-6.4-8.20231001.fc40.aar  31 MB/s | 328 kB     00:00    
(109/152): openldap-2.6.6-1.fc39.aarch64.rpm     22 MB/s | 251 kB     00:00    
(110/152): p11-kit-0.25.3-1.fc40.aarch64.rpm     42 MB/s | 495 kB     00:00    
(111/152): p11-kit-trust-0.25.3-1.fc40.aarch64.  19 MB/s | 141 kB     00:00    
(112/152): package-notes-srpm-macros-0.5-9.fc39 5.4 MB/s |  11 kB     00:00    
(113/152): pam-libs-1.5.3-8.fc40.aarch64.rpm     15 MB/s |  57 kB     00:00    
(114/152): patch-2.7.6-22.fc39.aarch64.rpm       32 MB/s | 123 kB     00:00    
(115/152): pcre2-10.42-2.fc40.aarch64.rpm        33 MB/s | 219 kB     00:00    
(116/152): pcre2-syntax-10.42-2.fc40.noarch.rpm  35 MB/s | 143 kB     00:00    
(117/152): pam-1.5.3-8.fc40.aarch64.rpm          25 MB/s | 557 kB     00:00    
(118/152): perl-srpm-macros-1-51.fc39.noarch.rp 2.4 MB/s | 8.0 kB     00:00    
(119/152): pkgconf-1.9.5-2.fc39.aarch64.rpm     8.9 MB/s |  42 kB     00:00    
(120/152): pkgconf-m4-1.9.5-2.fc39.noarch.rpm   5.2 MB/s |  14 kB     00:00    
(121/152): pkgconf-pkg-config-1.9.5-2.fc39.aarc 4.8 MB/s | 9.6 kB     00:00    
(122/152): popt-1.19-3.fc39.aarch64.rpm          16 MB/s |  66 kB     00:00    
(123/152): publicsuffix-list-dafsa-20230812-1.f  16 MB/s |  57 kB     00:00    
(124/152): pyproject-srpm-macros-1.10.0-1.fc40. 6.0 MB/s |  14 kB     00:00    
(125/152): python-srpm-macros-3.12-5.fc40.noarc 8.1 MB/s |  25 kB     00:00    
(126/152): qt5-srpm-macros-5.15.11-1.fc40.noarc 4.1 MB/s | 8.3 kB     00:00    
(127/152): qt6-srpm-macros-6.6.1-1.fc40.noarch. 4.0 MB/s | 8.6 kB     00:00    
(128/152): redhat-rpm-config-271-1.fc40.noarch.  14 MB/s |  81 kB     00:00    
(129/152): readline-8.2-4.fc39.aarch64.rpm       19 MB/s | 211 kB     00:00    
(130/152): rpm-build-4.19.0-3.fc40.aarch64.rpm   18 MB/s |  80 kB     00:00    
(131/152): rpm-build-libs-4.19.0-3.fc40.aarch64  31 MB/s |  92 kB     00:00    
(132/152): rpm-libs-4.19.0-3.fc40.aarch64.rpm    40 MB/s | 306 kB     00:00    
(133/152): rpm-4.19.0-3.fc40.aarch64.rpm         22 MB/s | 537 kB     00:00    
(134/152): rust-srpm-macros-25.2-2.fc40.noarch. 6.2 MB/s |  13 kB     00:00    
(135/152): openssl-libs-3.1.4-1.fc40.aarch64.rp  23 MB/s | 2.0 MB     00:00    
(136/152): setup-2.14.5-1.fc40.noarch.rpm        34 MB/s | 155 kB     00:00    
(137/152): sed-4.8-14.fc39.aarch64.rpm           34 MB/s | 304 kB     00:00    
(138/152): rpm-sequoia-1.5.0-2.fc40.aarch64.rpm  36 MB/s | 839 kB     00:00    
(139/152): systemd-libs-255-1.fc40.aarch64.rpm   45 MB/s | 680 kB     00:00    
(140/152): sqlite-libs-3.44.2-1.fc40.aarch64.rp  20 MB/s | 685 kB     00:00    
(141/152): unzip-6.0-62.fc39.aarch64.rpm         26 MB/s | 183 kB     00:00    
(142/152): tar-1.35-2.fc40.aarch64.rpm           39 MB/s | 854 kB     00:00    
(143/152): shadow-utils-4.14.0-2.fc40.aarch64.r  25 MB/s | 1.3 MB     00:00    
(144/152): util-linux-core-2.39.2-1.fc40.aarch6  45 MB/s | 490 kB     00:00    
(145/152): which-2.21-40.fc39.aarch64.rpm       6.1 MB/s |  42 kB     00:00    
(146/152): xxhash-libs-0.8.2-1.fc39.aarch64.rpm  11 MB/s |  35 kB     00:00    
(147/152): xz-libs-5.4.5-1.fc40.aarch64.rpm      17 MB/s | 107 kB     00:00    
(148/152): xz-5.4.5-1.fc40.aarch64.rpm           33 MB/s | 557 kB     00:00    
(149/152): zip-3.0-39.fc40.aarch64.rpm           26 MB/s | 262 kB     00:00    
(150/152): util-linux-2.39.2-1.fc40.aarch64.rpm  27 MB/s | 1.2 MB     00:00    
(151/152): zlib-1.2.13-5.fc40.aarch64.rpm       7.9 MB/s |  93 kB     00:00    
(152/152): zstd-1.5.5-4.fc39.aarch64.rpm         29 MB/s | 446 kB     00:00    
--------------------------------------------------------------------------------
Total                                            50 MB/s |  52 MB     00:01     
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0xA15B79CC:
 Userid     : "Fedora (40) <fedora-40-primary@fedoraproject.org>"
 Fingerprint: 115D F9AE F857 853E E844 5D0A 0727 707E A15B 79CC
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary
Key imported successfully
fedora                                          1.6 MB/s | 1.6 kB     00:00    
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary (0xA15B79CC) is already installed
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0x18B8E74C:
 Userid     : "Fedora (39) <fedora-39-primary@fedoraproject.org>"
 Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.18-6.fc39.aarch64                         1/1 
  Preparing        :                                                        1/1 
  Installing       : libgcc-13.2.1-6.fc40.aarch64                         1/152 
  Running scriptlet: libgcc-13.2.1-6.fc40.aarch64                         1/152 
  Installing       : crypto-policies-20231204-1.git1e3a2e4.fc40.noarc     2/152 
  Running scriptlet: crypto-policies-20231204-1.git1e3a2e4.fc40.noarc     2/152 
  Installing       : fedora-release-identity-basic-40-0.20.noarch         3/152 
  Installing       : fedora-repos-rawhide-40-0.2.noarch                   4/152 
  Installing       : fedora-gpg-keys-40-0.2.noarch                        5/152 
  Installing       : fedora-repos-40-0.2.noarch                           6/152 
  Installing       : fedora-release-common-40-0.20.noarch                 7/152 
  Installing       : fedora-release-40-0.20.noarch                        8/152 
  Installing       : setup-2.14.5-1.fc40.noarch                           9/152 
warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.14.5-1.fc40.noarch                           9/152 
  Installing       : filesystem-3.18-6.fc39.aarch64                      10/152 
  Installing       : basesystem-11-18.fc39.noarch                        11/152 
  Installing       : rust-srpm-macros-25.2-2.fc40.noarch                 12/152 
  Installing       : qt6-srpm-macros-6.6.1-1.fc40.noarch                 13/152 
  Installing       : qt5-srpm-macros-5.15.11-1.fc40.noarch               14/152 
  Installing       : publicsuffix-list-dafsa-20230812-1.fc40.noarch      15/152 
  Installing       : pkgconf-m4-1.9.5-2.fc39.noarch                      16/152 
  Installing       : perl-srpm-macros-1-51.fc39.noarch                   17/152 
  Installing       : pcre2-syntax-10.42-2.fc40.noarch                    18/152 
  Installing       : package-notes-srpm-macros-0.5-9.fc39.noarch         19/152 
  Installing       : openblas-srpm-macros-2-14.fc39.noarch               20/152 
  Installing       : ocaml-srpm-macros-9-1.fc40.noarch                   21/152 
  Installing       : ncurses-base-6.4-8.20231001.fc40.noarch             22/152 
  Installing       : glibc-gconv-extra-2.38.9000-26.fc40.aarch64         23/152 
  Running scriptlet: glibc-gconv-extra-2.38.9000-26.fc40.aarch64         23/152 
  Installing       : glibc-minimal-langpack-2.38.9000-26.fc40.aarch64    24/152 
  Installing       : glibc-common-2.38.9000-26.fc40.aarch64              25/152 
  Running scriptlet: glibc-2.38.9000-26.fc40.aarch64                     26/152 
  Installing       : glibc-2.38.9000-26.fc40.aarch64                     26/152 
  Running scriptlet: glibc-2.38.9000-26.fc40.aarch64                     26/152 
  Installing       : ncurses-libs-6.4-8.20231001.fc40.aarch64            27/152 
  Installing       : bash-5.2.21-2.fc40.aarch64                          28/152 
  Running scriptlet: bash-5.2.21-2.fc40.aarch64                          28/152 
  Installing       : zlib-1.2.13-5.fc40.aarch64                          29/152 
  Installing       : xz-libs-5.4.5-1.fc40.aarch64                        30/152 
  Installing       : bzip2-libs-1.0.8-16.fc39.aarch64                    31/152 
  Installing       : readline-8.2-4.fc39.aarch64                         32/152 
  Installing       : libstdc++-13.2.1-6.fc40.aarch64                     33/152 
  Installing       : libuuid-2.39.2-1.fc40.aarch64                       34/152 
  Installing       : libzstd-1.5.5-4.fc39.aarch64                        35/152 
  Installing       : elfutils-libelf-0.190-4.fc40.aarch64                36/152 
  Installing       : popt-1.19-3.fc39.aarch64                            37/152 
  Installing       : libblkid-2.39.2-1.fc40.aarch64                      38/152 
  Installing       : gmp-1:6.2.1-5.fc39.aarch64                          39/152 
  Installing       : libattr-2.5.1-9.fc40.aarch64                        40/152 
  Installing       : libacl-2.3.1-11.fc40.aarch64                        41/152 
  Installing       : libxcrypt-4.4.36-2.fc39.aarch64                     42/152 
  Installing       : gdbm-libs-1:1.23-4.fc39.aarch64                     43/152 
  Installing       : libeconf-0.5.2-1.fc40.aarch64                       44/152 
  Installing       : lz4-libs-1.9.4-4.fc39.aarch64                       45/152 
  Installing       : mpfr-4.2.1-1.fc40.aarch64                           46/152 
  Installing       : dwz-0.15-3.fc39.aarch64                             47/152 
  Installing       : unzip-6.0-62.fc39.aarch64                           48/152 
  Installing       : file-libs-5.45-1.fc40.aarch64                       49/152 
  Installing       : file-5.45-1.fc40.aarch64                            50/152 
  Installing       : alternatives-1.25-1.fc39.aarch64                    51/152 
  Installing       : jansson-2.13.1-7.fc39.aarch64                       52/152 
  Installing       : libcap-ng-0.8.3-8.fc40.aarch64                      53/152 
  Installing       : audit-libs-3.1.2-5.fc40.aarch64                     54/152 
  Installing       : pam-libs-1.5.3-8.fc40.aarch64                       55/152 
  Installing       : libcap-2.69-1.fc40.aarch64                          56/152 
  Installing       : systemd-libs-255-1.fc40.aarch64                     57/152 
  Installing       : libcom_err-1.47.0-2.fc39.aarch64                    58/152 
  Installing       : libsepol-3.6-0.rc2.1.fc40.aarch64                   59/152 
  Installing       : libsmartcols-2.39.2-1.fc40.aarch64                  60/152 
  Installing       : libtasn1-4.19.0-3.fc39.aarch64                      61/152 
  Installing       : libunistring-1.1-5.fc40.aarch64                     62/152 
  Installing       : libidn2-2.3.4-3.fc39.aarch64                        63/152 
  Installing       : lua-libs-5.4.6-3.fc39.aarch64                       64/152 
  Installing       : pcre2-10.42-2.fc40.aarch64                          65/152 
  Installing       : libselinux-3.6-0.rc2.1.fc40.aarch64                 66/152 
  Installing       : sed-4.8-14.fc39.aarch64                             67/152 
  Installing       : grep-3.11-5.fc40.aarch64                            68/152 
  Installing       : findutils-1:4.9.0-6.fc40.aarch64                    69/152 
  Installing       : xz-5.4.5-1.fc40.aarch64                             70/152 
  Installing       : libmount-2.39.2-1.fc40.aarch64                      71/152 
  Installing       : util-linux-core-2.39.2-1.fc40.aarch64               72/152 
  Installing       : libsemanage-3.6-0.rc2.1.fc40.aarch64                73/152 
  Installing       : shadow-utils-2:4.14.0-2.fc40.aarch64                74/152 
  Running scriptlet: libutempter-1.2.1-10.fc39.aarch64                   75/152 
  Installing       : libutempter-1.2.1-10.fc39.aarch64                   75/152 
  Installing       : tar-2:1.35-2.fc40.aarch64                           76/152 
  Installing       : libpsl-0.21.2-4.fc39.aarch64                        77/152 
  Installing       : zip-3.0-39.fc40.aarch64                             78/152 
  Installing       : zstd-1.5.5-4.fc39.aarch64                           79/152 
  Installing       : cyrus-sasl-lib-2.1.28-11.fc39.aarch64               80/152 
  Installing       : gdbm-1:1.23-4.fc39.aarch64                          81/152 
  Installing       : libfdisk-2.39.2-1.fc40.aarch64                      82/152 
  Installing       : bzip2-1.0.8-16.fc39.aarch64                         83/152 
  Installing       : libxml2-2.12.2-2.fc40.aarch64                       84/152 
  Installing       : sqlite-libs-3.44.2-1.fc40.aarch64                   85/152 
  Installing       : ed-1.19-4.fc39.aarch64                              86/152 
  Installing       : patch-2.7.6-22.fc39.aarch64                         87/152 
  Installing       : elfutils-default-yama-scope-0.190-4.fc40.noarch     88/152 
  Running scriptlet: elfutils-default-yama-scope-0.190-4.fc40.noarch     88/152 
  Installing       : cpio-2.14-5.fc40.aarch64                            89/152 
  Installing       : diffutils-3.10-3.fc39.aarch64                       90/152 
  Installing       : keyutils-libs-1.6.1-7.fc39.aarch64                  91/152 
  Installing       : libbrotli-1.1.0-1.fc40.aarch64                      92/152 
  Installing       : libffi-3.4.4-4.fc39.aarch64                         93/152 
  Installing       : p11-kit-0.25.3-1.fc40.aarch64                       94/152 
  Installing       : p11-kit-trust-0.25.3-1.fc40.aarch64                 95/152 
  Running scriptlet: p11-kit-trust-0.25.3-1.fc40.aarch64                 95/152 
  Installing       : libgomp-13.2.1-6.fc40.aarch64                       96/152 
  Installing       : libnghttp2-1.58.0-1.fc40.aarch64                    97/152 
  Installing       : libpkgconf-1.9.5-2.fc39.aarch64                     98/152 
  Installing       : pkgconf-1.9.5-2.fc39.aarch64                        99/152 
  Installing       : pkgconf-pkg-config-1.9.5-2.fc39.aarch64            100/152 
  Installing       : libsigsegv-2.14-5.fc39.aarch64                     101/152 
  Installing       : gawk-5.2.2-2.fc39.aarch64                          102/152 
  Installing       : libverto-0.3.2-6.fc39.aarch64                      103/152 
  Installing       : xxhash-libs-0.8.2-1.fc39.aarch64                   104/152 
  Installing       : libssh-config-0.10.5-2.fc39.noarch                 105/152 
  Installing       : kernel-srpm-macros-1.0-20.fc39.noarch              106/152 
  Installing       : gnat-srpm-macros-6-3.fc39.noarch                   107/152 
  Installing       : ghc-srpm-macros-1.6.1-3.fc40.noarch                108/152 
  Installing       : fpc-srpm-macros-1.3-8.fc39.noarch                  109/152 
  Installing       : coreutils-common-9.4-1.fc40.aarch64                110/152 
  Installing       : openssl-libs-1:3.1.4-1.fc40.aarch64                111/152 
  Installing       : coreutils-9.4-1.fc40.aarch64                       112/152 
  Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch   113/152 
  Installing       : ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch   113/152 
  Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch   113/152 
  Installing       : krb5-libs-1.21.2-2.fc40.aarch64                    114/152 
  Installing       : libtirpc-1.3.4-0.fc40.aarch64                      115/152 
  Running scriptlet: authselect-libs-1.4.3-1.fc40.aarch64               116/152 
  Installing       : authselect-libs-1.4.3-1.fc40.aarch64               116/152 
  Installing       : gzip-1.12-6.fc39.aarch64                           117/152 
  Installing       : cracklib-2.9.11-2.fc39.aarch64                     118/152 
  Installing       : libpwquality-1.4.5-6.fc39.aarch64                  119/152 
  Installing       : authselect-1.4.3-1.fc40.aarch64                    120/152 
  Installing       : libnsl2-2.0.0-6.fc39.aarch64                       121/152 
  Installing       : pam-1.5.3-8.fc40.aarch64                           122/152 
  Installing       : libssh-0.10.5-2.fc39.aarch64                       123/152 
  Installing       : libarchive-3.7.2-1.fc40.aarch64                    124/152 
  Installing       : libevent-2.1.12-9.fc39.aarch64                     125/152 
  Installing       : openldap-2.6.6-1.fc39.aarch64                      126/152 
  Installing       : libcurl-8.5.0-1.fc40.aarch64                       127/152 
  Installing       : elfutils-libs-0.190-4.fc40.aarch64                 128/152 
  Installing       : elfutils-debuginfod-client-0.190-4.fc40.aarch64    129/152 
  Installing       : binutils-gold-2.41-16.fc40.aarch64                 130/152 
  Running scriptlet: binutils-gold-2.41-16.fc40.aarch64                 130/152 
  Installing       : binutils-2.41-16.fc40.aarch64                      131/152 
  Running scriptlet: binutils-2.41-16.fc40.aarch64                      131/152 
  Installing       : elfutils-0.190-4.fc40.aarch64                      132/152 
  Installing       : gdb-minimal-14.1-1.fc40.aarch64                    133/152 
  Installing       : debugedit-5.0-12.fc40.aarch64                      134/152 
  Installing       : curl-8.5.0-1.fc40.aarch64                          135/152 
  Installing       : rpm-sequoia-1.5.0-2.fc40.aarch64                   136/152 
  Installing       : rpm-libs-4.19.0-3.fc40.aarch64                     137/152 
  Running scriptlet: rpm-4.19.0-3.fc40.aarch64                          138/152 
  Installing       : rpm-4.19.0-3.fc40.aarch64                          138/152 
  Installing       : efi-srpm-macros-5-9.fc39.noarch                    139/152 
  Installing       : lua-srpm-macros-1-9.fc39.noarch                    140/152 
  Installing       : rpm-build-libs-4.19.0-3.fc40.aarch64               141/152 
  Installing       : ansible-srpm-macros-1-11.fc39.noarch               142/152 
  Installing       : fonts-srpm-macros-1:2.0.5-12.fc39.noarch           143/152 
  Installing       : forge-srpm-macros-0.2.0-1.fc40.noarch              144/152 
  Installing       : go-srpm-macros-3.3.1-1.fc40.noarch                 145/152 
  Installing       : python-srpm-macros-3.12-5.fc40.noarch              146/152 
  Installing       : redhat-rpm-config-271-1.fc40.noarch                147/152 
  Installing       : rpm-build-4.19.0-3.fc40.aarch64                    148/152 
  Installing       : pyproject-srpm-macros-1.10.0-1.fc40.noarch         149/152 
  Installing       : util-linux-2.39.2-1.fc40.aarch64                   150/152 
  Installing       : which-2.21-40.fc39.aarch64                         151/152 
  Installing       : info-7.1-1.fc40.aarch64                            152/152 
  Running scriptlet: filesystem-3.18-6.fc39.aarch64                     152/152 
  Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch   152/152 
  Running scriptlet: authselect-libs-1.4.3-1.fc40.aarch64               152/152 
  Running scriptlet: rpm-4.19.0-3.fc40.aarch64                          152/152 
  Running scriptlet: info-7.1-1.fc40.aarch64                            152/152 

Installed:
  alternatives-1.25-1.fc39.aarch64                                              
  ansible-srpm-macros-1-11.fc39.noarch                                          
  audit-libs-3.1.2-5.fc40.aarch64                                               
  authselect-1.4.3-1.fc40.aarch64                                               
  authselect-libs-1.4.3-1.fc40.aarch64                                          
  basesystem-11-18.fc39.noarch                                                  
  bash-5.2.21-2.fc40.aarch64                                                    
  binutils-2.41-16.fc40.aarch64                                                 
  binutils-gold-2.41-16.fc40.aarch64                                            
  bzip2-1.0.8-16.fc39.aarch64                                                   
  bzip2-libs-1.0.8-16.fc39.aarch64                                              
  ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch                              
  coreutils-9.4-1.fc40.aarch64                                                  
  coreutils-common-9.4-1.fc40.aarch64                                           
  cpio-2.14-5.fc40.aarch64                                                      
  cracklib-2.9.11-2.fc39.aarch64                                                
  crypto-policies-20231204-1.git1e3a2e4.fc40.noarch                             
  curl-8.5.0-1.fc40.aarch64                                                     
  cyrus-sasl-lib-2.1.28-11.fc39.aarch64                                         
  debugedit-5.0-12.fc40.aarch64                                                 
  diffutils-3.10-3.fc39.aarch64                                                 
  dwz-0.15-3.fc39.aarch64                                                       
  ed-1.19-4.fc39.aarch64                                                        
  efi-srpm-macros-5-9.fc39.noarch                                               
  elfutils-0.190-4.fc40.aarch64                                                 
  elfutils-debuginfod-client-0.190-4.fc40.aarch64                               
  elfutils-default-yama-scope-0.190-4.fc40.noarch                               
  elfutils-libelf-0.190-4.fc40.aarch64                                          
  elfutils-libs-0.190-4.fc40.aarch64                                            
  fedora-gpg-keys-40-0.2.noarch                                                 
  fedora-release-40-0.20.noarch                                                 
  fedora-release-common-40-0.20.noarch                                          
  fedora-release-identity-basic-40-0.20.noarch                                  
  fedora-repos-40-0.2.noarch                                                    
  fedora-repos-rawhide-40-0.2.noarch                                            
  file-5.45-1.fc40.aarch64                                                      
  file-libs-5.45-1.fc40.aarch64                                                 
  filesystem-3.18-6.fc39.aarch64                                                
  findutils-1:4.9.0-6.fc40.aarch64                                              
  fonts-srpm-macros-1:2.0.5-12.fc39.noarch                                      
  forge-srpm-macros-0.2.0-1.fc40.noarch                                         
  fpc-srpm-macros-1.3-8.fc39.noarch                                             
  gawk-5.2.2-2.fc39.aarch64                                                     
  gdb-minimal-14.1-1.fc40.aarch64                                               
  gdbm-1:1.23-4.fc39.aarch64                                                    
  gdbm-libs-1:1.23-4.fc39.aarch64                                               
  ghc-srpm-macros-1.6.1-3.fc40.noarch                                           
  glibc-2.38.9000-26.fc40.aarch64                                               
  glibc-common-2.38.9000-26.fc40.aarch64                                        
  glibc-gconv-extra-2.38.9000-26.fc40.aarch64                                   
  glibc-minimal-langpack-2.38.9000-26.fc40.aarch64                              
  gmp-1:6.2.1-5.fc39.aarch64                                                    
  gnat-srpm-macros-6-3.fc39.noarch                                              
  go-srpm-macros-3.3.1-1.fc40.noarch                                            
  grep-3.11-5.fc40.aarch64                                                      
  gzip-1.12-6.fc39.aarch64                                                      
  info-7.1-1.fc40.aarch64                                                       
  jansson-2.13.1-7.fc39.aarch64                                                 
  kernel-srpm-macros-1.0-20.fc39.noarch                                         
  keyutils-libs-1.6.1-7.fc39.aarch64                                            
  krb5-libs-1.21.2-2.fc40.aarch64                                               
  libacl-2.3.1-11.fc40.aarch64                                                  
  libarchive-3.7.2-1.fc40.aarch64                                               
  libattr-2.5.1-9.fc40.aarch64                                                  
  libblkid-2.39.2-1.fc40.aarch64                                                
  libbrotli-1.1.0-1.fc40.aarch64                                                
  libcap-2.69-1.fc40.aarch64                                                    
  libcap-ng-0.8.3-8.fc40.aarch64                                                
  libcom_err-1.47.0-2.fc39.aarch64                                              
  libcurl-8.5.0-1.fc40.aarch64                                                  
  libeconf-0.5.2-1.fc40.aarch64                                                 
  libevent-2.1.12-9.fc39.aarch64                                                
  libfdisk-2.39.2-1.fc40.aarch64                                                
  libffi-3.4.4-4.fc39.aarch64                                                   
  libgcc-13.2.1-6.fc40.aarch64                                                  
  libgomp-13.2.1-6.fc40.aarch64                                                 
  libidn2-2.3.4-3.fc39.aarch64                                                  
  libmount-2.39.2-1.fc40.aarch64                                                
  libnghttp2-1.58.0-1.fc40.aarch64                                              
  libnsl2-2.0.0-6.fc39.aarch64                                                  
  libpkgconf-1.9.5-2.fc39.aarch64                                               
  libpsl-0.21.2-4.fc39.aarch64                                                  
  libpwquality-1.4.5-6.fc39.aarch64                                             
  libselinux-3.6-0.rc2.1.fc40.aarch64                                           
  libsemanage-3.6-0.rc2.1.fc40.aarch64                                          
  libsepol-3.6-0.rc2.1.fc40.aarch64                                             
  libsigsegv-2.14-5.fc39.aarch64                                                
  libsmartcols-2.39.2-1.fc40.aarch64                                            
  libssh-0.10.5-2.fc39.aarch64                                                  
  libssh-config-0.10.5-2.fc39.noarch                                            
  libstdc++-13.2.1-6.fc40.aarch64                                               
  libtasn1-4.19.0-3.fc39.aarch64                                                
  libtirpc-1.3.4-0.fc40.aarch64                                                 
  libunistring-1.1-5.fc40.aarch64                                               
  libutempter-1.2.1-10.fc39.aarch64                                             
  libuuid-2.39.2-1.fc40.aarch64                                                 
  libverto-0.3.2-6.fc39.aarch64                                                 
  libxcrypt-4.4.36-2.fc39.aarch64                                               
  libxml2-2.12.2-2.fc40.aarch64                                                 
  libzstd-1.5.5-4.fc39.aarch64                                                  
  lua-libs-5.4.6-3.fc39.aarch64                                                 
  lua-srpm-macros-1-9.fc39.noarch                                               
  lz4-libs-1.9.4-4.fc39.aarch64                                                 
  mpfr-4.2.1-1.fc40.aarch64                                                     
  ncurses-base-6.4-8.20231001.fc40.noarch                                       
  ncurses-libs-6.4-8.20231001.fc40.aarch64                                      
  ocaml-srpm-macros-9-1.fc40.noarch                                             
  openblas-srpm-macros-2-14.fc39.noarch                                         
  openldap-2.6.6-1.fc39.aarch64                                                 
  openssl-libs-1:3.1.4-1.fc40.aarch64                                           
  p11-kit-0.25.3-1.fc40.aarch64                                                 
  p11-kit-trust-0.25.3-1.fc40.aarch64                                           
  package-notes-srpm-macros-0.5-9.fc39.noarch                                   
  pam-1.5.3-8.fc40.aarch64                                                      
  pam-libs-1.5.3-8.fc40.aarch64                                                 
  patch-2.7.6-22.fc39.aarch64                                                   
  pcre2-10.42-2.fc40.aarch64                                                    
  pcre2-syntax-10.42-2.fc40.noarch                                              
  perl-srpm-macros-1-51.fc39.noarch                                             
  pkgconf-1.9.5-2.fc39.aarch64                                                  
  pkgconf-m4-1.9.5-2.fc39.noarch                                                
  pkgconf-pkg-config-1.9.5-2.fc39.aarch64                                       
  popt-1.19-3.fc39.aarch64                                                      
  publicsuffix-list-dafsa-20230812-1.fc40.noarch                                
  pyproject-srpm-macros-1.10.0-1.fc40.noarch                                    
  python-srpm-macros-3.12-5.fc40.noarch                                         
  qt5-srpm-macros-5.15.11-1.fc40.noarch                                         
  qt6-srpm-macros-6.6.1-1.fc40.noarch                                           
  readline-8.2-4.fc39.aarch64                                                   
  redhat-rpm-config-271-1.fc40.noarch                                           
  rpm-4.19.0-3.fc40.aarch64                                                     
  rpm-build-4.19.0-3.fc40.aarch64                                               
  rpm-build-libs-4.19.0-3.fc40.aarch64                                          
  rpm-libs-4.19.0-3.fc40.aarch64                                                
  rpm-sequoia-1.5.0-2.fc40.aarch64                                              
  rust-srpm-macros-25.2-2.fc40.noarch                                           
  sed-4.8-14.fc39.aarch64                                                       
  setup-2.14.5-1.fc40.noarch                                                    
  shadow-utils-2:4.14.0-2.fc40.aarch64                                          
  sqlite-libs-3.44.2-1.fc40.aarch64                                             
  systemd-libs-255-1.fc40.aarch64                                               
  tar-2:1.35-2.fc40.aarch64                                                     
  unzip-6.0-62.fc39.aarch64                                                     
  util-linux-2.39.2-1.fc40.aarch64                                              
  util-linux-core-2.39.2-1.fc40.aarch64                                         
  which-2.21-40.fc39.aarch64                                                    
  xxhash-libs-0.8.2-1.fc39.aarch64                                              
  xz-5.4.5-1.fc40.aarch64                                                       
  xz-libs-5.4.5-1.fc40.aarch64                                                  
  zip-3.0-39.fc40.aarch64                                                       
  zlib-1.2.13-5.fc40.aarch64                                                    
  zstd-1.5.5-4.fc39.aarch64                                                     

Complete!
Finish: installing minimal buildroot with dnf
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: alternatives-1.25-1.fc39.aarch64
ansible-srpm-macros-1-11.fc39.noarch
audit-libs-3.1.2-5.fc40.aarch64
authselect-1.4.3-1.fc40.aarch64
authselect-libs-1.4.3-1.fc40.aarch64
basesystem-11-18.fc39.noarch
bash-5.2.21-2.fc40.aarch64
binutils-2.41-16.fc40.aarch64
binutils-gold-2.41-16.fc40.aarch64
bzip2-1.0.8-16.fc39.aarch64
bzip2-libs-1.0.8-16.fc39.aarch64
ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch
coreutils-9.4-1.fc40.aarch64
coreutils-common-9.4-1.fc40.aarch64
cpio-2.14-5.fc40.aarch64
cracklib-2.9.11-2.fc39.aarch64
crypto-policies-20231204-1.git1e3a2e4.fc40.noarch
curl-8.5.0-1.fc40.aarch64
cyrus-sasl-lib-2.1.28-11.fc39.aarch64
debugedit-5.0-12.fc40.aarch64
diffutils-3.10-3.fc39.aarch64
dwz-0.15-3.fc39.aarch64
ed-1.19-4.fc39.aarch64
efi-srpm-macros-5-9.fc39.noarch
elfutils-0.190-4.fc40.aarch64
elfutils-debuginfod-client-0.190-4.fc40.aarch64
elfutils-default-yama-scope-0.190-4.fc40.noarch
elfutils-libelf-0.190-4.fc40.aarch64
elfutils-libs-0.190-4.fc40.aarch64
fedora-gpg-keys-40-0.2.noarch
fedora-release-40-0.20.noarch
fedora-release-common-40-0.20.noarch
fedora-release-identity-basic-40-0.20.noarch
fedora-repos-40-0.2.noarch
fedora-repos-rawhide-40-0.2.noarch
file-5.45-1.fc40.aarch64
file-libs-5.45-1.fc40.aarch64
filesystem-3.18-6.fc39.aarch64
findutils-4.9.0-6.fc40.aarch64
fonts-srpm-macros-2.0.5-12.fc39.noarch
forge-srpm-macros-0.2.0-1.fc40.noarch
fpc-srpm-macros-1.3-8.fc39.noarch
gawk-5.2.2-2.fc39.aarch64
gdb-minimal-14.1-1.fc40.aarch64
gdbm-1.23-4.fc39.aarch64
gdbm-libs-1.23-4.fc39.aarch64
ghc-srpm-macros-1.6.1-3.fc40.noarch
glibc-2.38.9000-26.fc40.aarch64
glibc-common-2.38.9000-26.fc40.aarch64
glibc-gconv-extra-2.38.9000-26.fc40.aarch64
glibc-minimal-langpack-2.38.9000-26.fc40.aarch64
gmp-6.2.1-5.fc39.aarch64
gnat-srpm-macros-6-3.fc39.noarch
go-srpm-macros-3.3.1-1.fc40.noarch
gpg-pubkey-18b8e74c-62f2920f
gpg-pubkey-a15b79cc-63d04c2c
grep-3.11-5.fc40.aarch64
gzip-1.12-6.fc39.aarch64
info-7.1-1.fc40.aarch64
jansson-2.13.1-7.fc39.aarch64
kernel-srpm-macros-1.0-20.fc39.noarch
keyutils-libs-1.6.1-7.fc39.aarch64
krb5-libs-1.21.2-2.fc40.aarch64
libacl-2.3.1-11.fc40.aarch64
libarchive-3.7.2-1.fc40.aarch64
libattr-2.5.1-9.fc40.aarch64
libblkid-2.39.2-1.fc40.aarch64
libbrotli-1.1.0-1.fc40.aarch64
libcap-2.69-1.fc40.aarch64
libcap-ng-0.8.3-8.fc40.aarch64
libcom_err-1.47.0-2.fc39.aarch64
libcurl-8.5.0-1.fc40.aarch64
libeconf-0.5.2-1.fc40.aarch64
libevent-2.1.12-9.fc39.aarch64
libfdisk-2.39.2-1.fc40.aarch64
libffi-3.4.4-4.fc39.aarch64
libgcc-13.2.1-6.fc40.aarch64
libgomp-13.2.1-6.fc40.aarch64
libidn2-2.3.4-3.fc39.aarch64
libmount-2.39.2-1.fc40.aarch64
libnghttp2-1.58.0-1.fc40.aarch64
libnsl2-2.0.0-6.fc39.aarch64
libpkgconf-1.9.5-2.fc39.aarch64
libpsl-0.21.2-4.fc39.aarch64
libpwquality-1.4.5-6.fc39.aarch64
libselinux-3.6-0.rc2.1.fc40.aarch64
libsemanage-3.6-0.rc2.1.fc40.aarch64
libsepol-3.6-0.rc2.1.fc40.aarch64
libsigsegv-2.14-5.fc39.aarch64
libsmartcols-2.39.2-1.fc40.aarch64
libssh-0.10.5-2.fc39.aarch64
libssh-config-0.10.5-2.fc39.noarch
libstdc++-13.2.1-6.fc40.aarch64
libtasn1-4.19.0-3.fc39.aarch64
libtirpc-1.3.4-0.fc40.aarch64
libunistring-1.1-5.fc40.aarch64
libutempter-1.2.1-10.fc39.aarch64
libuuid-2.39.2-1.fc40.aarch64
libverto-0.3.2-6.fc39.aarch64
libxcrypt-4.4.36-2.fc39.aarch64
libxml2-2.12.2-2.fc40.aarch64
libzstd-1.5.5-4.fc39.aarch64
lua-libs-5.4.6-3.fc39.aarch64
lua-srpm-macros-1-9.fc39.noarch
lz4-libs-1.9.4-4.fc39.aarch64
mpfr-4.2.1-1.fc40.aarch64
ncurses-base-6.4-8.20231001.fc40.noarch
ncurses-libs-6.4-8.20231001.fc40.aarch64
ocaml-srpm-macros-9-1.fc40.noarch
openblas-srpm-macros-2-14.fc39.noarch
openldap-2.6.6-1.fc39.aarch64
openssl-libs-3.1.4-1.fc40.aarch64
p11-kit-0.25.3-1.fc40.aarch64
p11-kit-trust-0.25.3-1.fc40.aarch64
package-notes-srpm-macros-0.5-9.fc39.noarch
pam-1.5.3-8.fc40.aarch64
pam-libs-1.5.3-8.fc40.aarch64
patch-2.7.6-22.fc39.aarch64
pcre2-10.42-2.fc40.aarch64
pcre2-syntax-10.42-2.fc40.noarch
perl-srpm-macros-1-51.fc39.noarch
pkgconf-1.9.5-2.fc39.aarch64
pkgconf-m4-1.9.5-2.fc39.noarch
pkgconf-pkg-config-1.9.5-2.fc39.aarch64
popt-1.19-3.fc39.aarch64
publicsuffix-list-dafsa-20230812-1.fc40.noarch
pyproject-srpm-macros-1.10.0-1.fc40.noarch
python-srpm-macros-3.12-5.fc40.noarch
qt5-srpm-macros-5.15.11-1.fc40.noarch
qt6-srpm-macros-6.6.1-1.fc40.noarch
readline-8.2-4.fc39.aarch64
redhat-rpm-config-271-1.fc40.noarch
rpm-4.19.0-3.fc40.aarch64
rpm-build-4.19.0-3.fc40.aarch64
rpm-build-libs-4.19.0-3.fc40.aarch64
rpm-libs-4.19.0-3.fc40.aarch64
rpm-sequoia-1.5.0-2.fc40.aarch64
rust-srpm-macros-25.2-2.fc40.noarch
sed-4.8-14.fc39.aarch64
setup-2.14.5-1.fc40.noarch
shadow-utils-4.14.0-2.fc40.aarch64
sqlite-libs-3.44.2-1.fc40.aarch64
systemd-libs-255-1.fc40.aarch64
tar-1.35-2.fc40.aarch64
unzip-6.0-62.fc39.aarch64
util-linux-2.39.2-1.fc40.aarch64
util-linux-core-2.39.2-1.fc40.aarch64
which-2.21-40.fc39.aarch64
xxhash-libs-0.8.2-1.fc39.aarch64
xz-5.4.5-1.fc40.aarch64
xz-libs-5.4.5-1.fc40.aarch64
zip-3.0-39.fc40.aarch64
zlib-1.2.13-5.fc40.aarch64
zstd-1.5.5-4.fc39.aarch64
Start: buildsrpm
Start: rpmbuild -bs
warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N)
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1689811200
Wrote: /builddir/build/SRPMS/mmseq-1.0.11-16.fc40.src.rpm

RPM build warnings:
    %patchN is deprecated (1 usages found), use %patch N (or %patch -P N)
Finish: rpmbuild -bs
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-aarch64-1702411319.400365/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-aarch64-1702411319.400365/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-aarch64-1702411319.400365/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-6klsy1ke/mmseq/mmseq.spec) Config(child) 1 minutes 2 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-1.0.11-16.fc40.src.rpm)  Config(fedora-rawhide-aarch64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1702411319.400365/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1702411319.400365/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-aarch64-1702411319.400365/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
Finish: chroot init
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.0-3.fc40.aarch64
  rpm-sequoia-1.5.0-2.fc40.aarch64
  python3-dnf-4.18.2-1.fc40.noarch
  python3-dnf-plugins-core-4.4.4-1.fc40.noarch
  yum-4.18.2-1.fc40.noarch
Start: build phase for mmseq-1.0.11-16.fc40.src.rpm
Start: build setup for mmseq-1.0.11-16.fc40.src.rpm
warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N)
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1689811200
Wrote: /builddir/build/SRPMS/mmseq-1.0.11-16.fc40.src.rpm

RPM build warnings:
    %patchN is deprecated (1 usages found), use %patch N (or %patch -P N)
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  46 kB/s | 1.5 kB     00:00    
fedora                                          106 kB/s |  11 kB     00:00    
Dependencies resolved.
================================================================================
 Package                      Arch     Version                 Repository  Size
================================================================================
Installing:
 armadillo-devel              aarch64  10.8.2-5.fc39           fedora     2.2 M
 boost-devel                  aarch64  1.83.0-0.fc40           copr_base   12 M
 flexiblas-devel              aarch64  3.3.1-5.fc39            fedora     116 k
 gcc-c++                      aarch64  13.2.1-6.fc40           fedora      12 M
 gsl-devel                    aarch64  2.7.1-5.fc39            fedora     653 k
 htslib-devel                 aarch64  1.15.1-3.fc39           fedora     105 k
 make                         aarch64  1:4.4.1-2.fc39          fedora     585 k
 perl-generators              noarch   1.16-3.fc39             fedora      16 k
 zlib-devel                   aarch64  1.2.13-5.fc40           fedora      45 k
Installing dependencies:
 SuperLU                      aarch64  6.0.1-1.fc40            fedora     171 k
 SuperLU-devel                aarch64  6.0.1-1.fc40            fedora      27 k
 annobin-docs                 noarch   12.33-1.fc40            fedora      91 k
 annobin-plugin-gcc           aarch64  12.33-1.fc40            fedora     958 k
 armadillo                    aarch64  10.8.2-5.fc39           fedora      33 k
 arpack                       aarch64  3.9.1-1.fc40            fedora     178 k
 arpack-devel                 aarch64  3.9.1-1.fc40            fedora      22 k
 autoconf                     noarch   2.71-7.fc40             fedora     733 k
 automake                     noarch   1.16.5-14.fc40          fedora     697 k
 boost                        aarch64  1.83.0-0.fc40           copr_base   14 k
 boost-atomic                 aarch64  1.83.0-0.fc40           copr_base   20 k
 boost-chrono                 aarch64  1.83.0-0.fc40           copr_base   26 k
 boost-container              aarch64  1.83.0-0.fc40           copr_base   40 k
 boost-context                aarch64  1.83.0-0.fc40           copr_base   17 k
 boost-contract               aarch64  1.83.0-0.fc40           copr_base   44 k
 boost-coroutine              aarch64  1.83.0-0.fc40           copr_base   21 k
 boost-date-time              aarch64  1.83.0-0.fc40           copr_base   16 k
 boost-fiber                  aarch64  1.83.0-0.fc40           copr_base   42 k
 boost-filesystem             aarch64  1.83.0-0.fc40           copr_base   64 k
 boost-graph                  aarch64  1.83.0-0.fc40           copr_base  143 k
 boost-iostreams              aarch64  1.83.0-0.fc40           copr_base   40 k
 boost-json                   aarch64  1.83.0-0.fc40           copr_base  141 k
 boost-locale                 aarch64  1.83.0-0.fc40           copr_base  196 k
 boost-log                    aarch64  1.83.0-0.fc40           copr_base  458 k
 boost-math                   aarch64  1.83.0-0.fc40           copr_base  259 k
 boost-nowide                 aarch64  1.83.0-0.fc40           copr_base   22 k
 boost-numpy3                 aarch64  1.83.0-0.fc40           copr_base   29 k
 boost-program-options        aarch64  1.83.0-0.fc40           copr_base  105 k
 boost-python3                aarch64  1.83.0-0.fc40           copr_base   90 k
 boost-random                 aarch64  1.83.0-0.fc40           copr_base   25 k
 boost-regex                  aarch64  1.83.0-0.fc40           copr_base  108 k
 boost-serialization          aarch64  1.83.0-0.fc40           copr_base  127 k
 boost-stacktrace             aarch64  1.83.0-0.fc40           copr_base   30 k
 boost-system                 aarch64  1.83.0-0.fc40           copr_base   16 k
 boost-test                   aarch64  1.83.0-0.fc40           copr_base  228 k
 boost-thread                 aarch64  1.83.0-0.fc40           copr_base   60 k
 boost-timer                  aarch64  1.83.0-0.fc40           copr_base   22 k
 boost-type_erasure           aarch64  1.83.0-0.fc40           copr_base   32 k
 boost-wave                   aarch64  1.83.0-0.fc40           copr_base  222 k
 cmake-filesystem             aarch64  3.27.7-1.fc40           fedora      19 k
 cpp                          aarch64  13.2.1-6.fc40           fedora     9.7 M
 emacs-filesystem             noarch   1:29.1-14.fc40          fedora     7.4 k
 expat                        aarch64  2.5.0-3.fc39            fedora     108 k
 flexiblas                    aarch64  3.3.1-5.fc39            fedora      33 k
 flexiblas-netlib             aarch64  3.3.1-5.fc39            fedora     2.6 M
 flexiblas-netlib64           aarch64  3.3.1-5.fc39            fedora     2.5 M
 flexiblas-openblas-openmp    aarch64  3.3.1-5.fc39            fedora      16 k
 flexiblas-openblas-openmp64  aarch64  3.3.1-5.fc39            fedora      16 k
 gc                           aarch64  8.2.2-4.fc39            fedora     110 k
 gcc                          aarch64  13.2.1-6.fc40           fedora      31 M
 gcc-gfortran                 aarch64  13.2.1-6.fc40           fedora      11 M
 gcc-plugin-annobin           aarch64  13.2.1-6.fc40           fedora      50 k
 glibc-devel                  aarch64  2.38.9000-26.fc40       fedora     594 k
 groff-base                   aarch64  1.23.0-3.fc40           fedora     1.1 M
 gsl                          aarch64  2.7.1-5.fc39            fedora     1.0 M
 guile22                      aarch64  2.2.7-9.fc39            fedora     6.5 M
 hdf5                         aarch64  1.12.1-15.fc40          fedora     2.1 M
 hdf5-devel                   aarch64  1.12.1-15.fc40          fedora     1.3 M
 htslib                       aarch64  1.15.1-3.fc39           fedora     480 k
 kernel-headers               aarch64  6.7.0-0.rc5.41.fc40     fedora     1.5 M
 libaec                       aarch64  1.0.6-5.fc39            fedora      41 k
 libaec-devel                 aarch64  1.0.6-5.fc39            fedora      12 k
 libasan                      aarch64  13.2.1-6.fc40           fedora     453 k
 libatomic                    aarch64  13.2.1-6.fc40           fedora      39 k
 libb2                        aarch64  0.98.1-9.fc39           fedora      24 k
 libgfortran                  aarch64  13.2.1-6.fc40           fedora     441 k
 libicu                       aarch64  73.2-2.fc39             fedora      10 M
 libicu-devel                 aarch64  73.2-2.fc39             fedora     925 k
 libmpc                       aarch64  1.3.1-3.fc39            fedora      72 k
 libstdc++-devel              aarch64  13.2.1-6.fc40           fedora     2.6 M
 libtool-ltdl                 aarch64  2.4.7-8.fc40            fedora      36 k
 libubsan                     aarch64  13.2.1-6.fc40           fedora     207 k
 libxcrypt-devel              aarch64  4.4.36-2.fc39           fedora      30 k
 m4                           aarch64  1.4.19-7.fc40           fedora     299 k
 metis                        aarch64  5.1.0.3-2.fc39          fedora     567 k
 mpdecimal                    aarch64  2.5.1-7.fc39            fedora      90 k
 ncurses                      aarch64  6.4-8.20231001.fc40     fedora     417 k
 openblas                     aarch64  0.3.25-1.fc40           fedora      38 k
 openblas-openmp              aarch64  0.3.25-1.fc40           fedora     3.9 M
 openblas-openmp64            aarch64  0.3.25-1.fc40           fedora     3.8 M
 perl-AutoLoader              noarch   5.74-503.fc40           fedora      21 k
 perl-B                       aarch64  1.88-503.fc40           fedora     178 k
 perl-Carp                    noarch   1.54-500.fc39           fedora      29 k
 perl-Class-Struct            noarch   0.68-503.fc40           fedora      22 k
 perl-Data-Dumper             aarch64  2.188-501.fc39          fedora      55 k
 perl-Digest                  noarch   1.20-500.fc39           fedora      25 k
 perl-Digest-MD5              aarch64  2.58-501.fc40           fedora      36 k
 perl-DynaLoader              aarch64  1.54-503.fc40           fedora      26 k
 perl-Encode                  aarch64  4:3.20-501.fc40         fedora     1.7 M
 perl-Errno                   aarch64  1.37-503.fc40           fedora      15 k
 perl-Exporter                noarch   5.77-500.fc39           fedora      31 k
 perl-Fcntl                   aarch64  1.15-503.fc40           fedora      21 k
 perl-Fedora-VSP              noarch   0.001-32.fc39           fedora      23 k
 perl-File-Basename           noarch   2.86-503.fc40           fedora      17 k
 perl-File-Compare            noarch   1.100.700-503.fc40      fedora      13 k
 perl-File-Copy               noarch   2.41-503.fc40           fedora      20 k
 perl-File-Find               noarch   1.43-503.fc40           fedora      26 k
 perl-File-Path               noarch   2.18-501.fc40           fedora      35 k
 perl-File-Temp               noarch   1:0.231.100-501.fc40    fedora      59 k
 perl-File-stat               noarch   1.13-503.fc40           fedora      17 k
 perl-FileHandle              noarch   2.05-503.fc40           fedora      16 k
 perl-Getopt-Long             noarch   1:2.57-1.fc40           fedora      63 k
 perl-Getopt-Std              noarch   1.13-503.fc40           fedora      16 k
 perl-HTTP-Tiny               noarch   0.088-3.fc39            fedora      56 k
 perl-IO                      aarch64  1.52-503.fc40           fedora      83 k
 perl-IO-Socket-IP            noarch   0.42-1.fc39             fedora      42 k
 perl-IO-Socket-SSL           noarch   2.084-1.fc40            fedora     225 k
 perl-IPC-Open3               noarch   1.22-503.fc40           fedora      22 k
 perl-MIME-Base64             aarch64  3.16-501.fc40           fedora      30 k
 perl-Mozilla-CA              noarch   20230821-1.fc40         fedora      13 k
 perl-Net-SSLeay              aarch64  1.92-10.fc39            fedora     356 k
 perl-POSIX                   aarch64  2.13-503.fc40           fedora      98 k
 perl-PathTools               aarch64  3.89-500.fc39           fedora      88 k
 perl-Pod-Escapes             noarch   1:1.07-501.fc40         fedora      19 k
 perl-Pod-Perldoc             noarch   3.28.01-501.fc39        fedora      86 k
 perl-Pod-Simple              noarch   1:3.45-4.fc39           fedora     218 k
 perl-Pod-Usage               noarch   4:2.03-500.fc39         fedora      39 k
 perl-Scalar-List-Utils       aarch64  5:1.63-500.fc39         fedora      71 k
 perl-SelectSaver             noarch   1.02-503.fc40           fedora      12 k
 perl-Socket                  aarch64  4:2.037-3.fc39          fedora      56 k
 perl-Storable                aarch64  1:3.32-500.fc39         fedora      97 k
 perl-Symbol                  noarch   1.09-503.fc40           fedora      14 k
 perl-Term-ANSIColor          noarch   5.01-502.fc40           fedora      47 k
 perl-Term-Cap                noarch   1.18-500.fc39           fedora      22 k
 perl-Text-ParseWords         noarch   3.31-500.fc39           fedora      16 k
 perl-Text-Tabs+Wrap          noarch   2023.0511-3.fc39        fedora      22 k
 perl-Thread-Queue            noarch   3.14-501.fc40           fedora      21 k
 perl-Time-Local              noarch   2:1.350-3.fc39          fedora      34 k
 perl-URI                     noarch   5.21-1.fc40             fedora     125 k
 perl-base                    noarch   2.27-503.fc40           fedora      16 k
 perl-constant                noarch   1.33-501.fc39           fedora      22 k
 perl-if                      noarch   0.61.000-503.fc40       fedora      14 k
 perl-interpreter             aarch64  4:5.38.2-503.fc40       fedora      72 k
 perl-libnet                  noarch   3.15-501.fc39           fedora     129 k
 perl-libs                    aarch64  4:5.38.2-503.fc40       fedora     2.3 M
 perl-locale                  noarch   1.10-503.fc40           fedora      14 k
 perl-macros                  noarch   4:5.38.2-503.fc40       fedora      13 k
 perl-mro                     aarch64  1.28-503.fc40           fedora      29 k
 perl-overload                noarch   1.37-503.fc40           fedora      46 k
 perl-overloading             noarch   0.02-503.fc40           fedora      13 k
 perl-parent                  noarch   1:0.241-500.fc39        fedora      14 k
 perl-podlators               noarch   1:5.01-500.fc39         fedora     125 k
 perl-threads                 aarch64  1:2.36-500.fc39         fedora      57 k
 perl-threads-shared          aarch64  1.68-500.fc39           fedora      44 k
 perl-vars                    noarch   1.05-503.fc40           fedora      13 k
 python-pip-wheel             noarch   23.2.1-1.fc39           fedora     1.5 M
 python3                      aarch64  3.12.1-1.fc40           fedora      27 k
 python3-libs                 aarch64  3.12.1-1.fc40           fedora     9.1 M
 python3-numpy                aarch64  1:1.26.0-2.fc40         fedora     6.6 M
 tzdata                       noarch   2023c-4.fc40            fedora     717 k

Transaction Summary
================================================================================
Install  159 Packages

Total download size: 154 M
Installed size: 691 M
Downloading Packages:
(1/159): boost-1.83.0-0.fc40.aarch64.rpm        800 kB/s |  14 kB     00:00    
(2/159): boost-chrono-1.83.0-0.fc40.aarch64.rpm 1.3 MB/s |  26 kB     00:00    
(3/159): boost-atomic-1.83.0-0.fc40.aarch64.rpm 1.0 MB/s |  20 kB     00:00    
(4/159): boost-container-1.83.0-0.fc40.aarch64.  20 MB/s |  40 kB     00:00    
(5/159): boost-context-1.83.0-0.fc40.aarch64.rp 6.8 MB/s |  17 kB     00:00    
(6/159): boost-contract-1.83.0-0.fc40.aarch64.r  17 MB/s |  44 kB     00:00    
(7/159): boost-coroutine-1.83.0-0.fc40.aarch64. 8.0 MB/s |  21 kB     00:00    
(8/159): boost-date-time-1.83.0-0.fc40.aarch64. 6.3 MB/s |  16 kB     00:00    
(9/159): boost-fiber-1.83.0-0.fc40.aarch64.rpm  8.8 MB/s |  42 kB     00:00    
(10/159): boost-filesystem-1.83.0-0.fc40.aarch6  14 MB/s |  64 kB     00:00    
(11/159): boost-graph-1.83.0-0.fc40.aarch64.rpm  43 MB/s | 143 kB     00:00    
(12/159): boost-iostreams-1.83.0-0.fc40.aarch64  11 MB/s |  40 kB     00:00    
(13/159): boost-json-1.83.0-0.fc40.aarch64.rpm   21 MB/s | 141 kB     00:00    
(14/159): boost-locale-1.83.0-0.fc40.aarch64.rp  27 MB/s | 196 kB     00:00    
(15/159): boost-log-1.83.0-0.fc40.aarch64.rpm    50 MB/s | 458 kB     00:00    
(16/159): boost-math-1.83.0-0.fc40.aarch64.rpm   27 MB/s | 259 kB     00:00    
(17/159): boost-nowide-1.83.0-0.fc40.aarch64.rp 2.2 MB/s |  22 kB     00:00    
(18/159): boost-numpy3-1.83.0-0.fc40.aarch64.rp 2.9 MB/s |  29 kB     00:00    
(19/159): boost-program-options-1.83.0-0.fc40.a  22 MB/s | 105 kB     00:00    
(20/159): boost-python3-1.83.0-0.fc40.aarch64.r  16 MB/s |  90 kB     00:00    
(21/159): boost-random-1.83.0-0.fc40.aarch64.rp 6.9 MB/s |  25 kB     00:00    
(22/159): boost-regex-1.83.0-0.fc40.aarch64.rpm  27 MB/s | 108 kB     00:00    
(23/159): boost-serialization-1.83.0-0.fc40.aar  48 MB/s | 127 kB     00:00    
(24/159): boost-stacktrace-1.83.0-0.fc40.aarch6 9.1 MB/s |  30 kB     00:00    
(25/159): boost-system-1.83.0-0.fc40.aarch64.rp 7.5 MB/s |  16 kB     00:00    
(26/159): boost-test-1.83.0-0.fc40.aarch64.rpm   59 MB/s | 228 kB     00:00    
(27/159): boost-thread-1.83.0-0.fc40.aarch64.rp  14 MB/s |  60 kB     00:00    
(28/159): boost-timer-1.83.0-0.fc40.aarch64.rpm 6.6 MB/s |  22 kB     00:00    
(29/159): boost-type_erasure-1.83.0-0.fc40.aarc 9.2 MB/s |  32 kB     00:00    
(30/159): boost-wave-1.83.0-0.fc40.aarch64.rpm   55 MB/s | 222 kB     00:00    
(31/159): boost-devel-1.83.0-0.fc40.aarch64.rpm 151 MB/s |  12 MB     00:00    
(32/159): SuperLU-6.0.1-1.fc40.aarch64.rpm      8.3 MB/s | 171 kB     00:00    
(33/159): annobin-docs-12.33-1.fc40.noarch.rpm   24 MB/s |  91 kB     00:00    
(34/159): armadillo-10.8.2-5.fc39.aarch64.rpm    14 MB/s |  33 kB     00:00    
(35/159): annobin-plugin-gcc-12.33-1.fc40.aarch  44 MB/s | 958 kB     00:00    
(36/159): arpack-3.9.1-1.fc40.aarch64.rpm        73 MB/s | 178 kB     00:00    
(37/159): SuperLU-devel-6.0.1-1.fc40.aarch64.rp 332 kB/s |  27 kB     00:00    
(38/159): armadillo-devel-10.8.2-5.fc39.aarch64  35 MB/s | 2.2 MB     00:00    
(39/159): arpack-devel-3.9.1-1.fc40.aarch64.rpm 354 kB/s |  22 kB     00:00    
(40/159): cmake-filesystem-3.27.7-1.fc40.aarch6 7.6 MB/s |  19 kB     00:00    
(41/159): automake-1.16.5-14.fc40.noarch.rpm     28 MB/s | 697 kB     00:00    
(42/159): autoconf-2.71-7.fc40.noarch.rpm        25 MB/s | 733 kB     00:00    
(43/159): emacs-filesystem-29.1-14.fc40.noarch. 4.5 MB/s | 7.4 kB     00:00    
(44/159): flexiblas-3.3.1-5.fc39.aarch64.rpm     11 MB/s |  33 kB     00:00    
(45/159): expat-2.5.0-3.fc39.aarch64.rpm         24 MB/s | 108 kB     00:00    
(46/159): flexiblas-devel-3.3.1-5.fc39.aarch64.  22 MB/s | 116 kB     00:00    
(47/159): flexiblas-netlib64-3.3.1-5.fc39.aarch 241 MB/s | 2.5 MB     00:00    
(48/159): flexiblas-openblas-openmp-3.3.1-5.fc3 6.6 MB/s |  16 kB     00:00    
(49/159): flexiblas-openblas-openmp64-3.3.1-5.f 6.3 MB/s |  16 kB     00:00    
(50/159): gc-8.2.2-4.fc39.aarch64.rpm            17 MB/s | 110 kB     00:00    
(51/159): flexiblas-netlib-3.3.1-5.fc39.aarch64  46 MB/s | 2.6 MB     00:00    
(52/159): cpp-13.2.1-6.fc40.aarch64.rpm          50 MB/s | 9.7 MB     00:00    
(53/159): gcc-13.2.1-6.fc40.aarch64.rpm          94 MB/s |  31 MB     00:00    
(54/159): gcc-plugin-annobin-13.2.1-6.fc40.aarc 6.7 MB/s |  50 kB     00:00    
(55/159): glibc-devel-2.38.9000-26.fc40.aarch64  39 MB/s | 594 kB     00:00    
(56/159): gcc-gfortran-13.2.1-6.fc40.aarch64.rp  47 MB/s |  11 MB     00:00    
(57/159): groff-base-1.23.0-3.fc40.aarch64.rpm   22 MB/s | 1.1 MB     00:00    
(58/159): gsl-devel-2.7.1-5.fc39.aarch64.rpm    148 MB/s | 653 kB     00:00    
(59/159): gsl-2.7.1-5.fc39.aarch64.rpm           60 MB/s | 1.0 MB     00:00    
(60/159): hdf5-1.12.1-15.fc40.aarch64.rpm       213 MB/s | 2.1 MB     00:00    
(61/159): gcc-c++-13.2.1-6.fc40.aarch64.rpm      29 MB/s |  12 MB     00:00    
(62/159): hdf5-devel-1.12.1-15.fc40.aarch64.rpm  53 MB/s | 1.3 MB     00:00    
(63/159): htslib-devel-1.15.1-3.fc39.aarch64.rp 1.2 MB/s | 105 kB     00:00    
(64/159): htslib-1.15.1-3.fc39.aarch64.rpm      4.4 MB/s | 480 kB     00:00    
(65/159): libaec-1.0.6-5.fc39.aarch64.rpm        21 MB/s |  41 kB     00:00    
(66/159): libaec-devel-1.0.6-5.fc39.aarch64.rpm 3.9 MB/s |  12 kB     00:00    
(67/159): libasan-13.2.1-6.fc40.aarch64.rpm      37 MB/s | 453 kB     00:00    
(68/159): libatomic-13.2.1-6.fc40.aarch64.rpm    11 MB/s |  39 kB     00:00    
(69/159): libb2-0.98.1-9.fc39.aarch64.rpm        10 MB/s |  24 kB     00:00    
(70/159): libgfortran-13.2.1-6.fc40.aarch64.rpm  42 MB/s | 441 kB     00:00    
(71/159): kernel-headers-6.7.0-0.rc5.41.fc40.aa  29 MB/s | 1.5 MB     00:00    
(72/159): guile22-2.2.7-9.fc39.aarch64.rpm       34 MB/s | 6.5 MB     00:00    
(73/159): libicu-devel-73.2-2.fc39.aarch64.rpm   46 MB/s | 925 kB     00:00    
(74/159): libmpc-1.3.1-3.fc39.aarch64.rpm        17 MB/s |  72 kB     00:00    
(75/159): libtool-ltdl-2.4.7-8.fc40.aarch64.rpm  14 MB/s |  36 kB     00:00    
(76/159): libubsan-13.2.1-6.fc40.aarch64.rpm     17 MB/s | 207 kB     00:00    
(77/159): libxcrypt-devel-4.4.36-2.fc39.aarch64 9.7 MB/s |  30 kB     00:00    
(78/159): m4-1.4.19-7.fc40.aarch64.rpm           36 MB/s | 299 kB     00:00    
(79/159): make-4.4.1-2.fc39.aarch64.rpm          41 MB/s | 585 kB     00:00    
(80/159): metis-5.1.0.3-2.fc39.aarch64.rpm       67 MB/s | 567 kB     00:00    
(81/159): libstdc++-devel-13.2.1-6.fc40.aarch64  47 MB/s | 2.6 MB     00:00    
(82/159): mpdecimal-2.5.1-7.fc39.aarch64.rpm     14 MB/s |  90 kB     00:00    
(83/159): openblas-0.3.25-1.fc40.aarch64.rpm     14 MB/s |  38 kB     00:00    
(84/159): ncurses-6.4-8.20231001.fc40.aarch64.r  19 MB/s | 417 kB     00:00    
(85/159): openblas-openmp64-0.3.25-1.fc40.aarch 174 MB/s | 3.8 MB     00:00    
(86/159): perl-AutoLoader-5.74-503.fc40.noarch. 8.0 MB/s |  21 kB     00:00    
(87/159): perl-B-1.88-503.fc40.aarch64.rpm       33 MB/s | 178 kB     00:00    
(88/159): perl-Carp-1.54-500.fc39.noarch.rpm     11 MB/s |  29 kB     00:00    
(89/159): perl-Class-Struct-0.68-503.fc40.noarc 7.8 MB/s |  22 kB     00:00    
(90/159): perl-Data-Dumper-2.188-501.fc39.aarch  20 MB/s |  55 kB     00:00    
(91/159): perl-Digest-1.20-500.fc39.noarch.rpm  8.5 MB/s |  25 kB     00:00    
(92/159): perl-Digest-MD5-2.58-501.fc40.aarch64  12 MB/s |  36 kB     00:00    
(93/159): perl-DynaLoader-1.54-503.fc40.aarch64 8.3 MB/s |  26 kB     00:00    
(94/159): openblas-openmp-0.3.25-1.fc40.aarch64  43 MB/s | 3.9 MB     00:00    
(95/159): perl-Errno-1.37-503.fc40.aarch64.rpm  5.6 MB/s |  15 kB     00:00    
(96/159): perl-Exporter-5.77-500.fc39.noarch.rp  10 MB/s |  31 kB     00:00    
(97/159): perl-Fcntl-1.15-503.fc40.aarch64.rpm  8.6 MB/s |  21 kB     00:00    
(98/159): perl-Fedora-VSP-0.001-32.fc39.noarch.  11 MB/s |  23 kB     00:00    
(99/159): perl-File-Basename-2.86-503.fc40.noar 3.7 MB/s |  17 kB     00:00    
(100/159): perl-Encode-3.20-501.fc40.aarch64.rp  42 MB/s | 1.7 MB     00:00    
(101/159): perl-File-Compare-1.100.700-503.fc40 2.5 MB/s |  13 kB     00:00    
(102/159): perl-File-Copy-2.41-503.fc40.noarch. 8.1 MB/s |  20 kB     00:00    
(103/159): perl-File-Find-1.43-503.fc40.noarch. 8.4 MB/s |  26 kB     00:00    
(104/159): perl-File-Path-2.18-501.fc40.noarch.  12 MB/s |  35 kB     00:00    
(105/159): perl-File-Temp-0.231.100-501.fc40.no  16 MB/s |  59 kB     00:00    
(106/159): perl-File-stat-1.13-503.fc40.noarch. 5.3 MB/s |  17 kB     00:00    
(107/159): perl-FileHandle-2.05-503.fc40.noarch 6.0 MB/s |  16 kB     00:00    
(108/159): perl-Getopt-Std-1.13-503.fc40.noarch 6.1 MB/s |  16 kB     00:00    
(109/159): perl-Getopt-Long-2.57-1.fc40.noarch.  13 MB/s |  63 kB     00:00    
(110/159): perl-HTTP-Tiny-0.088-3.fc39.noarch.r  11 MB/s |  56 kB     00:00    
(111/159): perl-IO-1.52-503.fc40.aarch64.rpm     15 MB/s |  83 kB     00:00    
(112/159): perl-IO-Socket-IP-0.42-1.fc39.noarch 9.9 MB/s |  42 kB     00:00    
(113/159): perl-IO-Socket-SSL-2.084-1.fc40.noar  53 MB/s | 225 kB     00:00    
(114/159): perl-IPC-Open3-1.22-503.fc40.noarch. 7.5 MB/s |  22 kB     00:00    
(115/159): perl-Mozilla-CA-20230821-1.fc40.noar 7.0 MB/s |  13 kB     00:00    
(116/159): perl-MIME-Base64-3.16-501.fc40.aarch 6.8 MB/s |  30 kB     00:00    
(117/159): perl-POSIX-2.13-503.fc40.aarch64.rpm  21 MB/s |  98 kB     00:00    
(118/159): perl-Net-SSLeay-1.92-10.fc39.aarch64  37 MB/s | 356 kB     00:00    
(119/159): perl-PathTools-3.89-500.fc39.aarch64  15 MB/s |  88 kB     00:00    
(120/159): perl-Pod-Escapes-1.07-501.fc40.noarc 6.6 MB/s |  19 kB     00:00    
(121/159): perl-Pod-Perldoc-3.28.01-501.fc39.no  14 MB/s |  86 kB     00:00    
(122/159): perl-Pod-Simple-3.45-4.fc39.noarch.r  29 MB/s | 218 kB     00:00    
(123/159): libicu-73.2-2.fc39.aarch64.rpm        40 MB/s |  10 MB     00:00    
(124/159): perl-Pod-Usage-2.03-500.fc39.noarch. 2.8 MB/s |  39 kB     00:00    
(125/159): perl-Scalar-List-Utils-1.63-500.fc39 6.4 MB/s |  71 kB     00:00    
(126/159): perl-SelectSaver-1.02-503.fc40.noarc 3.8 MB/s |  12 kB     00:00    
(127/159): perl-Socket-2.037-3.fc39.aarch64.rpm  17 MB/s |  56 kB     00:00    
(128/159): perl-Storable-3.32-500.fc39.aarch64.  18 MB/s |  97 kB     00:00    
(129/159): perl-Symbol-1.09-503.fc40.noarch.rpm 4.3 MB/s |  14 kB     00:00    
(130/159): perl-Term-ANSIColor-5.01-502.fc40.no  15 MB/s |  47 kB     00:00    
(131/159): perl-Text-ParseWords-3.31-500.fc39.n 6.7 MB/s |  16 kB     00:00    
(132/159): perl-Term-Cap-1.18-500.fc39.noarch.r 6.8 MB/s |  22 kB     00:00    
(133/159): perl-Text-Tabs+Wrap-2023.0511-3.fc39 8.3 MB/s |  22 kB     00:00    
(134/159): perl-Thread-Queue-3.14-501.fc40.noar 4.0 MB/s |  21 kB     00:00    
(135/159): perl-Time-Local-1.350-3.fc39.noarch. 6.0 MB/s |  34 kB     00:00    
(136/159): perl-URI-5.21-1.fc40.noarch.rpm       15 MB/s | 125 kB     00:00    
(137/159): perl-base-2.27-503.fc40.noarch.rpm   2.8 MB/s |  16 kB     00:00    
(138/159): perl-constant-1.33-501.fc39.noarch.r 3.9 MB/s |  22 kB     00:00    
(139/159): perl-generators-1.16-3.fc39.noarch.r 4.3 MB/s |  16 kB     00:00    
(140/159): perl-if-0.61.000-503.fc40.noarch.rpm 5.1 MB/s |  14 kB     00:00    
(141/159): perl-libnet-3.15-501.fc39.noarch.rpm  40 MB/s | 129 kB     00:00    
(142/159): perl-interpreter-5.38.2-503.fc40.aar  15 MB/s |  72 kB     00:00    
(143/159): perl-locale-1.10-503.fc40.noarch.rpm 7.4 MB/s |  14 kB     00:00    
(144/159): perl-macros-5.38.2-503.fc40.noarch.r 2.3 MB/s |  13 kB     00:00    
(145/159): perl-mro-1.28-503.fc40.aarch64.rpm   4.1 MB/s |  29 kB     00:00    
(146/159): perl-overload-1.37-503.fc40.noarch.r 9.6 MB/s |  46 kB     00:00    
(147/159): perl-overloading-0.02-503.fc40.noarc 6.4 MB/s |  13 kB     00:00    
(148/159): perl-parent-0.241-500.fc39.noarch.rp 5.4 MB/s |  14 kB     00:00    
(149/159): perl-podlators-5.01-500.fc39.noarch.  34 MB/s | 125 kB     00:00    
(150/159): perl-threads-2.36-500.fc39.aarch64.r  14 MB/s |  57 kB     00:00    
(151/159): perl-threads-shared-1.68-500.fc39.aa  15 MB/s |  44 kB     00:00    
(152/159): perl-vars-1.05-503.fc40.noarch.rpm   3.8 MB/s |  13 kB     00:00    
(153/159): python3-3.12.1-1.fc40.aarch64.rpm    6.9 MB/s |  27 kB     00:00    
(154/159): perl-libs-5.38.2-503.fc40.aarch64.rp  44 MB/s | 2.3 MB     00:00    
(155/159): python-pip-wheel-23.2.1-1.fc39.noarc  33 MB/s | 1.5 MB     00:00    
(156/159): tzdata-2023c-4.fc40.noarch.rpm        43 MB/s | 717 kB     00:00    
(157/159): zlib-devel-1.2.13-5.fc40.aarch64.rpm  15 MB/s |  45 kB     00:00    
(158/159): python3-numpy-1.26.0-2.fc40.aarch64.  41 MB/s | 6.6 MB     00:00    
(159/159): python3-libs-3.12.1-1.fc40.aarch64.r  44 MB/s | 9.1 MB     00:00    
--------------------------------------------------------------------------------
Total                                           109 MB/s | 154 MB     00:01     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
  Installing       : boost-system-1.83.0-0.fc40.aarch64                   1/159 
  Installing       : libgfortran-13.2.1-6.fc40.aarch64                    2/159 
  Installing       : boost-chrono-1.83.0-0.fc40.aarch64                   3/159 
  Installing       : boost-thread-1.83.0-0.fc40.aarch64                   4/159 
  Installing       : libicu-73.2-2.fc39.aarch64                           5/159 
  Installing       : libmpc-1.3.1-3.fc39.aarch64                          6/159 
  Installing       : boost-regex-1.83.0-0.fc40.aarch64                    7/159 
  Installing       : boost-context-1.83.0-0.fc40.aarch64                  8/159 
  Installing       : boost-atomic-1.83.0-0.fc40.aarch64                   9/159 
  Installing       : boost-filesystem-1.83.0-0.fc40.aarch64              10/159 
  Installing       : openblas-0.3.25-1.fc40.aarch64                      11/159 
  Installing       : libstdc++-devel-13.2.1-6.fc40.aarch64               12/159 
  Installing       : libaec-1.0.6-5.fc39.aarch64                         13/159 
  Installing       : hdf5-1.12.1-15.fc40.aarch64                         14/159 
  Installing       : boost-date-time-1.83.0-0.fc40.aarch64               15/159 
  Installing       : boost-container-1.83.0-0.fc40.aarch64               16/159 
  Installing       : boost-json-1.83.0-0.fc40.aarch64                    17/159 
  Installing       : boost-wave-1.83.0-0.fc40.aarch64                    18/159 
  Installing       : libaec-devel-1.0.6-5.fc39.aarch64                   19/159 
  Installing       : openblas-openmp-0.3.25-1.fc40.aarch64               20/159 
  Installing       : openblas-openmp64-0.3.25-1.fc40.aarch64             21/159 
  Installing       : flexiblas-netlib-3.3.1-5.fc39.aarch64               22/159 
  Installing       : flexiblas-openblas-openmp-3.3.1-5.fc39.aarch64      23/159 
  Installing       : flexiblas-netlib64-3.3.1-5.fc39.aarch64             24/159 
  Installing       : flexiblas-openblas-openmp64-3.3.1-5.fc39.aarch64    25/159 
  Installing       : flexiblas-3.3.1-5.fc39.aarch64                      26/159 
  Installing       : arpack-3.9.1-1.fc40.aarch64                         27/159 
  Installing       : arpack-devel-3.9.1-1.fc40.aarch64                   28/159 
  Installing       : flexiblas-devel-3.3.1-5.fc39.aarch64                29/159 
  Installing       : boost-fiber-1.83.0-0.fc40.aarch64                   30/159 
  Installing       : boost-log-1.83.0-0.fc40.aarch64                     31/159 
  Installing       : boost-coroutine-1.83.0-0.fc40.aarch64               32/159 
  Installing       : boost-graph-1.83.0-0.fc40.aarch64                   33/159 
  Installing       : cpp-13.2.1-6.fc40.aarch64                           34/159 
  Installing       : boost-locale-1.83.0-0.fc40.aarch64                  35/159 
  Installing       : libicu-devel-73.2-2.fc39.aarch64                    36/159 
  Installing       : boost-type_erasure-1.83.0-0.fc40.aarch64            37/159 
  Installing       : boost-timer-1.83.0-0.fc40.aarch64                   38/159 
  Installing       : zlib-devel-1.2.13-5.fc40.aarch64                    39/159 
  Installing       : tzdata-2023c-4.fc40.noarch                          40/159 
  Installing       : python-pip-wheel-23.2.1-1.fc39.noarch               41/159 
  Installing       : ncurses-6.4-8.20231001.fc40.aarch64                 42/159 
  Installing       : mpdecimal-2.5.1-7.fc39.aarch64                      43/159 
  Installing       : metis-5.1.0.3-2.fc39.aarch64                        44/159 
  Installing       : SuperLU-6.0.1-1.fc40.aarch64                        45/159 
  Installing       : armadillo-10.8.2-5.fc39.aarch64                     46/159 
  Installing       : m4-1.4.19-7.fc40.aarch64                            47/159 
  Installing       : libubsan-13.2.1-6.fc40.aarch64                      48/159 
  Installing       : libtool-ltdl-2.4.7-8.fc40.aarch64                   49/159 
  Installing       : libb2-0.98.1-9.fc39.aarch64                         50/159 
  Installing       : libatomic-13.2.1-6.fc40.aarch64                     51/159 
  Installing       : libasan-13.2.1-6.fc40.aarch64                       52/159 
  Installing       : kernel-headers-6.7.0-0.rc5.41.fc40.aarch64          53/159 
  Installing       : libxcrypt-devel-4.4.36-2.fc39.aarch64               54/159 
  Installing       : glibc-devel-2.38.9000-26.fc40.aarch64               55/159 
  Installing       : htslib-1.15.1-3.fc39.aarch64                        56/159 
  Installing       : gsl-2.7.1-5.fc39.aarch64                            57/159 
  Running scriptlet: groff-base-1.23.0-3.fc40.aarch64                    58/159 
  Installing       : groff-base-1.23.0-3.fc40.aarch64                    58/159 
  Running scriptlet: groff-base-1.23.0-3.fc40.aarch64                    58/159 
  Installing       : perl-Digest-1.20-500.fc39.noarch                    59/159 
  Installing       : perl-Digest-MD5-2.58-501.fc40.aarch64               60/159 
  Installing       : perl-B-1.88-503.fc40.aarch64                        61/159 
  Installing       : perl-FileHandle-2.05-503.fc40.noarch                62/159 
  Installing       : perl-Data-Dumper-2.188-501.fc39.aarch64             63/159 
  Installing       : perl-libnet-3.15-501.fc39.noarch                    64/159 
  Installing       : perl-AutoLoader-5.74-503.fc40.noarch                65/159 
  Installing       : perl-URI-5.21-1.fc40.noarch                         66/159 
  Installing       : perl-Text-Tabs+Wrap-2023.0511-3.fc39.noarch         67/159 
  Installing       : perl-Mozilla-CA-20230821-1.fc40.noarch              68/159 
  Installing       : perl-if-0.61.000-503.fc40.noarch                    69/159 
  Installing       : perl-locale-1.10-503.fc40.noarch                    70/159 
  Installing       : perl-IO-Socket-IP-0.42-1.fc39.noarch                71/159 
  Installing       : perl-Time-Local-2:1.350-3.fc39.noarch               72/159 
  Installing       : perl-File-Path-2.18-501.fc40.noarch                 73/159 
  Installing       : perl-IO-Socket-SSL-2.084-1.fc40.noarch              74/159 
  Installing       : perl-Net-SSLeay-1.92-10.fc39.aarch64                75/159 
  Installing       : perl-Pod-Escapes-1:1.07-501.fc40.noarch             76/159 
  Installing       : perl-Class-Struct-0.68-503.fc40.noarch              77/159 
  Installing       : perl-Term-ANSIColor-5.01-502.fc40.noarch            78/159 
  Installing       : perl-POSIX-2.13-503.fc40.aarch64                    79/159 
  Installing       : perl-IPC-Open3-1.22-503.fc40.noarch                 80/159 
  Installing       : perl-File-Temp-1:0.231.100-501.fc40.noarch          81/159 
  Installing       : perl-HTTP-Tiny-0.088-3.fc39.noarch                  82/159 
  Installing       : perl-Term-Cap-1.18-500.fc39.noarch                  83/159 
  Installing       : perl-Pod-Simple-1:3.45-4.fc39.noarch                84/159 
  Installing       : perl-Socket-4:2.037-3.fc39.aarch64                  85/159 
  Installing       : perl-SelectSaver-1.02-503.fc40.noarch               86/159 
  Installing       : perl-Symbol-1.09-503.fc40.noarch                    87/159 
  Installing       : perl-File-stat-1.13-503.fc40.noarch                 88/159 
  Installing       : perl-podlators-1:5.01-500.fc39.noarch               89/159 
  Installing       : perl-Pod-Perldoc-3.28.01-501.fc39.noarch            90/159 
  Installing       : perl-Fcntl-1.15-503.fc40.aarch64                    91/159 
  Installing       : perl-Text-ParseWords-3.31-500.fc39.noarch           92/159 
  Installing       : perl-base-2.27-503.fc40.noarch                      93/159 
  Installing       : perl-mro-1.28-503.fc40.aarch64                      94/159 
  Installing       : perl-IO-1.52-503.fc40.aarch64                       95/159 
  Installing       : perl-overloading-0.02-503.fc40.noarch               96/159 
  Installing       : perl-Pod-Usage-4:2.03-500.fc39.noarch               97/159 
  Installing       : perl-Errno-1.37-503.fc40.aarch64                    98/159 
  Installing       : perl-File-Basename-2.86-503.fc40.noarch             99/159 
  Installing       : perl-Getopt-Std-1.13-503.fc40.noarch               100/159 
  Installing       : perl-MIME-Base64-3.16-501.fc40.aarch64             101/159 
  Installing       : perl-Scalar-List-Utils-5:1.63-500.fc39.aarch64     102/159 
  Installing       : perl-constant-1.33-501.fc39.noarch                 103/159 
  Installing       : perl-Storable-1:3.32-500.fc39.aarch64              104/159 
  Installing       : perl-overload-1.37-503.fc40.noarch                 105/159 
  Installing       : perl-parent-1:0.241-500.fc39.noarch                106/159 
  Installing       : perl-vars-1.05-503.fc40.noarch                     107/159 
  Installing       : perl-Getopt-Long-1:2.57-1.fc40.noarch              108/159 
  Installing       : perl-Carp-1.54-500.fc39.noarch                     109/159 
  Installing       : perl-Exporter-5.77-500.fc39.noarch                 110/159 
  Installing       : perl-PathTools-3.89-500.fc39.aarch64               111/159 
  Installing       : perl-DynaLoader-1.54-503.fc40.aarch64              112/159 
  Installing       : perl-Encode-4:3.20-501.fc40.aarch64                113/159 
  Installing       : perl-libs-4:5.38.2-503.fc40.aarch64                114/159 
  Installing       : perl-interpreter-4:5.38.2-503.fc40.aarch64         115/159 
  Installing       : perl-threads-1:2.36-500.fc39.aarch64               116/159 
  Installing       : perl-threads-shared-1.68-500.fc39.aarch64          117/159 
  Installing       : perl-Thread-Queue-3.14-501.fc40.noarch             118/159 
  Installing       : perl-macros-4:5.38.2-503.fc40.noarch               119/159 
  Installing       : perl-Fedora-VSP-0.001-32.fc39.noarch               120/159 
  Installing       : perl-File-Compare-1.100.700-503.fc40.noarch        121/159 
  Installing       : perl-File-Copy-2.41-503.fc40.noarch                122/159 
  Installing       : perl-File-Find-1.43-503.fc40.noarch                123/159 
  Installing       : gc-8.2.2-4.fc39.aarch64                            124/159 
  Installing       : guile22-2.2.7-9.fc39.aarch64                       125/159 
  Installing       : make-1:4.4.1-2.fc39.aarch64                        126/159 
  Installing       : gcc-13.2.1-6.fc40.aarch64                          127/159 
  Running scriptlet: gcc-13.2.1-6.fc40.aarch64                          127/159 
  Installing       : gcc-gfortran-13.2.1-6.fc40.aarch64                 128/159 
  Installing       : hdf5-devel-1.12.1-15.fc40.aarch64                  129/159 
  Installing       : expat-2.5.0-3.fc39.aarch64                         130/159 
  Installing       : python3-3.12.1-1.fc40.aarch64                      131/159 
  Installing       : python3-libs-3.12.1-1.fc40.aarch64                 132/159 
  Installing       : boost-python3-1.83.0-0.fc40.aarch64                133/159 
  Installing       : python3-numpy-1:1.26.0-2.fc40.aarch64              134/159 
  Installing       : boost-numpy3-1.83.0-0.fc40.aarch64                 135/159 
  Installing       : emacs-filesystem-1:29.1-14.fc40.noarch             136/159 
  Installing       : autoconf-2.71-7.fc40.noarch                        137/159 
  Installing       : automake-1.16.5-14.fc40.noarch                     138/159 
  Installing       : cmake-filesystem-3.27.7-1.fc40.aarch64             139/159 
  Installing       : SuperLU-devel-6.0.1-1.fc40.aarch64                 140/159 
  Installing       : annobin-docs-12.33-1.fc40.noarch                   141/159 
  Installing       : boost-test-1.83.0-0.fc40.aarch64                   142/159 
  Installing       : boost-stacktrace-1.83.0-0.fc40.aarch64             143/159 
  Installing       : boost-serialization-1.83.0-0.fc40.aarch64          144/159 
  Installing       : boost-random-1.83.0-0.fc40.aarch64                 145/159 
  Installing       : boost-program-options-1.83.0-0.fc40.aarch64        146/159 
  Installing       : boost-nowide-1.83.0-0.fc40.aarch64                 147/159 
  Installing       : boost-math-1.83.0-0.fc40.aarch64                   148/159 
  Installing       : boost-iostreams-1.83.0-0.fc40.aarch64              149/159 
  Installing       : boost-contract-1.83.0-0.fc40.aarch64               150/159 
  Installing       : boost-1.83.0-0.fc40.aarch64                        151/159 
  Installing       : boost-devel-1.83.0-0.fc40.aarch64                  152/159 
  Installing       : annobin-plugin-gcc-12.33-1.fc40.aarch64            153/159 
  Running scriptlet: annobin-plugin-gcc-12.33-1.fc40.aarch64            153/159 
  Installing       : armadillo-devel-10.8.2-5.fc39.aarch64              154/159 
  Installing       : gsl-devel-2.7.1-5.fc39.aarch64                     155/159 
  Installing       : gcc-c++-13.2.1-6.fc40.aarch64                      156/159 
  Installing       : gcc-plugin-annobin-13.2.1-6.fc40.aarch64           157/159 
  Running scriptlet: gcc-plugin-annobin-13.2.1-6.fc40.aarch64           157/159 
  Installing       : perl-generators-1.16-3.fc39.noarch                 158/159 
  Installing       : htslib-devel-1.15.1-3.fc39.aarch64                 159/159 
  Running scriptlet: htslib-devel-1.15.1-3.fc39.aarch64                 159/159 

Installed:
  SuperLU-6.0.1-1.fc40.aarch64                                                  
  SuperLU-devel-6.0.1-1.fc40.aarch64                                            
  annobin-docs-12.33-1.fc40.noarch                                              
  annobin-plugin-gcc-12.33-1.fc40.aarch64                                       
  armadillo-10.8.2-5.fc39.aarch64                                               
  armadillo-devel-10.8.2-5.fc39.aarch64                                         
  arpack-3.9.1-1.fc40.aarch64                                                   
  arpack-devel-3.9.1-1.fc40.aarch64                                             
  autoconf-2.71-7.fc40.noarch                                                   
  automake-1.16.5-14.fc40.noarch                                                
  boost-1.83.0-0.fc40.aarch64                                                   
  boost-atomic-1.83.0-0.fc40.aarch64                                            
  boost-chrono-1.83.0-0.fc40.aarch64                                            
  boost-container-1.83.0-0.fc40.aarch64                                         
  boost-context-1.83.0-0.fc40.aarch64                                           
  boost-contract-1.83.0-0.fc40.aarch64                                          
  boost-coroutine-1.83.0-0.fc40.aarch64                                         
  boost-date-time-1.83.0-0.fc40.aarch64                                         
  boost-devel-1.83.0-0.fc40.aarch64                                             
  boost-fiber-1.83.0-0.fc40.aarch64                                             
  boost-filesystem-1.83.0-0.fc40.aarch64                                        
  boost-graph-1.83.0-0.fc40.aarch64                                             
  boost-iostreams-1.83.0-0.fc40.aarch64                                         
  boost-json-1.83.0-0.fc40.aarch64                                              
  boost-locale-1.83.0-0.fc40.aarch64                                            
  boost-log-1.83.0-0.fc40.aarch64                                               
  boost-math-1.83.0-0.fc40.aarch64                                              
  boost-nowide-1.83.0-0.fc40.aarch64                                            
  boost-numpy3-1.83.0-0.fc40.aarch64                                            
  boost-program-options-1.83.0-0.fc40.aarch64                                   
  boost-python3-1.83.0-0.fc40.aarch64                                           
  boost-random-1.83.0-0.fc40.aarch64                                            
  boost-regex-1.83.0-0.fc40.aarch64                                             
  boost-serialization-1.83.0-0.fc40.aarch64                                     
  boost-stacktrace-1.83.0-0.fc40.aarch64                                        
  boost-system-1.83.0-0.fc40.aarch64                                            
  boost-test-1.83.0-0.fc40.aarch64                                              
  boost-thread-1.83.0-0.fc40.aarch64                                            
  boost-timer-1.83.0-0.fc40.aarch64                                             
  boost-type_erasure-1.83.0-0.fc40.aarch64                                      
  boost-wave-1.83.0-0.fc40.aarch64                                              
  cmake-filesystem-3.27.7-1.fc40.aarch64                                        
  cpp-13.2.1-6.fc40.aarch64                                                     
  emacs-filesystem-1:29.1-14.fc40.noarch                                        
  expat-2.5.0-3.fc39.aarch64                                                    
  flexiblas-3.3.1-5.fc39.aarch64                                                
  flexiblas-devel-3.3.1-5.fc39.aarch64                                          
  flexiblas-netlib-3.3.1-5.fc39.aarch64                                         
  flexiblas-netlib64-3.3.1-5.fc39.aarch64                                       
  flexiblas-openblas-openmp-3.3.1-5.fc39.aarch64                                
  flexiblas-openblas-openmp64-3.3.1-5.fc39.aarch64                              
  gc-8.2.2-4.fc39.aarch64                                                       
  gcc-13.2.1-6.fc40.aarch64                                                     
  gcc-c++-13.2.1-6.fc40.aarch64                                                 
  gcc-gfortran-13.2.1-6.fc40.aarch64                                            
  gcc-plugin-annobin-13.2.1-6.fc40.aarch64                                      
  glibc-devel-2.38.9000-26.fc40.aarch64                                         
  groff-base-1.23.0-3.fc40.aarch64                                              
  gsl-2.7.1-5.fc39.aarch64                                                      
  gsl-devel-2.7.1-5.fc39.aarch64                                                
  guile22-2.2.7-9.fc39.aarch64                                                  
  hdf5-1.12.1-15.fc40.aarch64                                                   
  hdf5-devel-1.12.1-15.fc40.aarch64                                             
  htslib-1.15.1-3.fc39.aarch64                                                  
  htslib-devel-1.15.1-3.fc39.aarch64                                            
  kernel-headers-6.7.0-0.rc5.41.fc40.aarch64                                    
  libaec-1.0.6-5.fc39.aarch64                                                   
  libaec-devel-1.0.6-5.fc39.aarch64                                             
  libasan-13.2.1-6.fc40.aarch64                                                 
  libatomic-13.2.1-6.fc40.aarch64                                               
  libb2-0.98.1-9.fc39.aarch64                                                   
  libgfortran-13.2.1-6.fc40.aarch64                                             
  libicu-73.2-2.fc39.aarch64                                                    
  libicu-devel-73.2-2.fc39.aarch64                                              
  libmpc-1.3.1-3.fc39.aarch64                                                   
  libstdc++-devel-13.2.1-6.fc40.aarch64                                         
  libtool-ltdl-2.4.7-8.fc40.aarch64                                             
  libubsan-13.2.1-6.fc40.aarch64                                                
  libxcrypt-devel-4.4.36-2.fc39.aarch64                                         
  m4-1.4.19-7.fc40.aarch64                                                      
  make-1:4.4.1-2.fc39.aarch64                                                   
  metis-5.1.0.3-2.fc39.aarch64                                                  
  mpdecimal-2.5.1-7.fc39.aarch64                                                
  ncurses-6.4-8.20231001.fc40.aarch64                                           
  openblas-0.3.25-1.fc40.aarch64                                                
  openblas-openmp-0.3.25-1.fc40.aarch64                                         
  openblas-openmp64-0.3.25-1.fc40.aarch64                                       
  perl-AutoLoader-5.74-503.fc40.noarch                                          
  perl-B-1.88-503.fc40.aarch64                                                  
  perl-Carp-1.54-500.fc39.noarch                                                
  perl-Class-Struct-0.68-503.fc40.noarch                                        
  perl-Data-Dumper-2.188-501.fc39.aarch64                                       
  perl-Digest-1.20-500.fc39.noarch                                              
  perl-Digest-MD5-2.58-501.fc40.aarch64                                         
  perl-DynaLoader-1.54-503.fc40.aarch64                                         
  perl-Encode-4:3.20-501.fc40.aarch64                                           
  perl-Errno-1.37-503.fc40.aarch64                                              
  perl-Exporter-5.77-500.fc39.noarch                                            
  perl-Fcntl-1.15-503.fc40.aarch64                                              
  perl-Fedora-VSP-0.001-32.fc39.noarch                                          
  perl-File-Basename-2.86-503.fc40.noarch                                       
  perl-File-Compare-1.100.700-503.fc40.noarch                                   
  perl-File-Copy-2.41-503.fc40.noarch                                           
  perl-File-Find-1.43-503.fc40.noarch                                           
  perl-File-Path-2.18-501.fc40.noarch                                           
  perl-File-Temp-1:0.231.100-501.fc40.noarch                                    
  perl-File-stat-1.13-503.fc40.noarch                                           
  perl-FileHandle-2.05-503.fc40.noarch                                          
  perl-Getopt-Long-1:2.57-1.fc40.noarch                                         
  perl-Getopt-Std-1.13-503.fc40.noarch                                          
  perl-HTTP-Tiny-0.088-3.fc39.noarch                                            
  perl-IO-1.52-503.fc40.aarch64                                                 
  perl-IO-Socket-IP-0.42-1.fc39.noarch                                          
  perl-IO-Socket-SSL-2.084-1.fc40.noarch                                        
  perl-IPC-Open3-1.22-503.fc40.noarch                                           
  perl-MIME-Base64-3.16-501.fc40.aarch64                                        
  perl-Mozilla-CA-20230821-1.fc40.noarch                                        
  perl-Net-SSLeay-1.92-10.fc39.aarch64                                          
  perl-POSIX-2.13-503.fc40.aarch64                                              
  perl-PathTools-3.89-500.fc39.aarch64                                          
  perl-Pod-Escapes-1:1.07-501.fc40.noarch                                       
  perl-Pod-Perldoc-3.28.01-501.fc39.noarch                                      
  perl-Pod-Simple-1:3.45-4.fc39.noarch                                          
  perl-Pod-Usage-4:2.03-500.fc39.noarch                                         
  perl-Scalar-List-Utils-5:1.63-500.fc39.aarch64                                
  perl-SelectSaver-1.02-503.fc40.noarch                                         
  perl-Socket-4:2.037-3.fc39.aarch64                                            
  perl-Storable-1:3.32-500.fc39.aarch64                                         
  perl-Symbol-1.09-503.fc40.noarch                                              
  perl-Term-ANSIColor-5.01-502.fc40.noarch                                      
  perl-Term-Cap-1.18-500.fc39.noarch                                            
  perl-Text-ParseWords-3.31-500.fc39.noarch                                     
  perl-Text-Tabs+Wrap-2023.0511-3.fc39.noarch                                   
  perl-Thread-Queue-3.14-501.fc40.noarch                                        
  perl-Time-Local-2:1.350-3.fc39.noarch                                         
  perl-URI-5.21-1.fc40.noarch                                                   
  perl-base-2.27-503.fc40.noarch                                                
  perl-constant-1.33-501.fc39.noarch                                            
  perl-generators-1.16-3.fc39.noarch                                            
  perl-if-0.61.000-503.fc40.noarch                                              
  perl-interpreter-4:5.38.2-503.fc40.aarch64                                    
  perl-libnet-3.15-501.fc39.noarch                                              
  perl-libs-4:5.38.2-503.fc40.aarch64                                           
  perl-locale-1.10-503.fc40.noarch                                              
  perl-macros-4:5.38.2-503.fc40.noarch                                          
  perl-mro-1.28-503.fc40.aarch64                                                
  perl-overload-1.37-503.fc40.noarch                                            
  perl-overloading-0.02-503.fc40.noarch                                         
  perl-parent-1:0.241-500.fc39.noarch                                           
  perl-podlators-1:5.01-500.fc39.noarch                                         
  perl-threads-1:2.36-500.fc39.aarch64                                          
  perl-threads-shared-1.68-500.fc39.aarch64                                     
  perl-vars-1.05-503.fc40.noarch                                                
  python-pip-wheel-23.2.1-1.fc39.noarch                                         
  python3-3.12.1-1.fc40.aarch64                                                 
  python3-libs-3.12.1-1.fc40.aarch64                                            
  python3-numpy-1:1.26.0-2.fc40.aarch64                                         
  tzdata-2023c-4.fc40.noarch                                                    
  zlib-devel-1.2.13-5.fc40.aarch64                                              

Complete!
Finish: build setup for mmseq-1.0.11-16.fc40.src.rpm
Start: rpmbuild mmseq-1.0.11-16.fc40.src.rpm
warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N)
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1689811200
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.lweN4g
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/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
+ rm -rf /builddir/build/BUILD/mmseq-1.0.11-SPECPARTS
+ /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-SPECPARTS
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ echo 'Patch #2 (mmseq-zlib.patch):'
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.JSln14
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,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 -j4 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 offsetGTF.cpp -o ../bin/offsetGTF
offsetGTF.cpp: In function ‘int main(int, char**)’:
offsetGTF.cpp:115:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  115 |       while(gff_ind < gff_positions[chrom].size()) {
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
offsetGTF.cpp:117:57: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} [-Wsign-compare]
  117 |               pos + tokens[3].size() - tokens[4].size() >= gff_positions[chrom][gff_ind]) {
offsetGTF.cpp:114:11: warning: unused variable ‘curoff’ [-Wunused-variable]
  114 |       int curoff=offset;
      |           ^~~~~~
offsetGTF.cpp:150:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  150 |       while(gff_ind < gff_positions[prevchrom].size()) {
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
offsetGTF.cpp:163:53: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} [-Wsign-compare]
  163 |           pos + tokens[3].size() - tokens[4].size() >= gff_positions[chrom][gff_ind]) {
offsetGTF.cpp:177:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  177 |     while(gff_ind < gff_positions[chrom].size() && gff_positions[chrom][gff_ind] <= pos) {
      |           ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
offsetGTF.cpp:235:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  235 |     for(int i=5; i < tokens.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~
offsetGTF.cpp:237:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  237 |       if(i < tokens.size()-1) {
      |          ~~^~~~~~~~~~~~~~~~~
offsetGTF.cpp:108:7: warning: unused variable ‘gff_pos’ [-Wunused-variable]
  108 |   int gff_pos= -1;
      |       ^~~~~~~
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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++) {
      |                      ~~^~~~~~~~~~~~~~~
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 -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O2 bms.cpp bms.hpp -c bms.cpp
hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema0()’:
hitsio.cpp:163:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  163 |         for(int i = 0; i < transcriptName.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema0()’:
hitsio.cpp:184:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  184 |         for(int i = 0; i < currentReadTranscripts.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema1()’:
hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   24 |         if (VAL > numeric_limits<uint32_t>::max()) { \
      |                 ^
hitsio.cpp:191:9: note: in expansion of macro ‘WRITE_UINT’
  191 |         WRITE_UINT(ofs, hitsfileSchema);
      |         ^~~~~~~~~~
hitsio.cpp:193:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  193 |         for(int i = 0; i < transcriptName.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘std::map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
   24 |         if (VAL > numeric_limits<uint32_t>::max()) { \
hitsio.cpp:196:17: note: in expansion of macro ‘WRITE_UINT’
  196 |                 WRITE_UINT(ofs, transcriptTrueLength[transcriptName[i] ])
      |                 ^~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema1()’:
hitsio.cpp:236:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  236 |         for(int i = 0; i < currentReadTranscripts.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileReader::readHeaderSchema1(std::vector<std::__cxx11::basic_string<char> >*, std::map<std::__cxx11::basic_string<char>, double>*, std::map<std::__cxx11::basic_string<char>, int>*, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >*, std::vector<std::vector<std::__cxx11::basic_string<char> > >*)’:
hitsio.cpp:356:16: warning: unused variable ‘nextStrLen’ [-Wunused-variable]
  356 |         size_t nextStrLen;
      |                ^~~~~~~~~~
hitsio.cpp: In member function ‘bool HitsfileReader::readReadMapRecordTranscriptID(std::string&)’:
hitsio.cpp:447:1: warning: control reaches end of non-void function [-Wreturn-type]
  447 | }
      | ^
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 -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 fasta.o extract_transcripts.cpp -o ../bin/extract_transcripts
g++ -DVERSION=1.0.11 -DARMA_64BIT_WORD -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 uh.o sokal.o mmcollapse.cpp -o ../bin/mmcollapse -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
extract_transcripts.cpp: In function ‘int main(int, char**)’:
extract_transcripts.cpp:122:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  122 |       for(int i=0; i < tokens2.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~
extract_transcripts.cpp:169:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  169 |     for(int i=0; i < tokens.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~
extract_transcripts.cpp:195:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  195 |       for(int i=0; i < it->starts()->size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~
extract_transcripts.cpp:203:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  203 |       while(faline < stitch.size()) {
      |             ~~~~~~~^~~~~~~~~~~~~~~
extract_transcripts.cpp:108:7: warning: unused variable ‘line’ [-Wunused-variable]
  108 |   int line=0;
      |       ^~~~
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++) {
      |                ~~^~~~~~~~~~~~~
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;
      |         ^~~~~~~
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 -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 sokal.o uh.o hitsio.o mmseq.cpp -o ../bin/mmseq -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 fasta.o hitsio.o bam2hits.cpp -o ../bin/bam2hits -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
mmseq.cpp: In function ‘std::vector<double> meanvar(std::vector<double>, double, double)’:
mmseq.cpp:130:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  130 |   for(int i=0;i < v.size(); i++) {
      |               ~~^~~~~~~~~~
mmseq.cpp: In function ‘int main(int, char**)’:
mmseq.cpp:244:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  244 |       for(int i=0; i < tokens.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~
mmseq.cpp:423:20: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  423 |       if(M.size1() < m ) factor1=2;
      |          ~~~~~~~~~~^~~
mmseq.cpp:424:20: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  424 |       if(M.size2() < n ) factor2=2;
      |          ~~~~~~~~~~^~~
mmseq.cpp:594:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  594 |   for(unsigned t=0; t < n; t++)  {
      |                     ~~^~~
mmseq.cpp:736:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  736 |     for(unsigned t=0; t < n; t++)
      |                       ~~^~~
mmseq.cpp:765:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  765 |       for(unsigned t=0; t < n; t++)
      |                         ~~^~~
mmseq.cpp:774:11: warning: unused variable ‘threadid’ [-Wunused-variable]
  774 |       int threadid=OMP_GET_THREAD_NUM;
      |           ^~~~~~~~
mmseq.cpp:829:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  829 |   for(unsigned t=0; t < n; t++)
      |                     ~~^~~
mmseq.cpp:912:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  912 |       for(unsigned t=0; t < n; t++) {
      |                         ~~^~~
mmseq.cpp:940:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  940 |   for(int i=0; i < identical_transcripts.size() * trace_length; i++) mu_trace_identical[i]=0;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:961:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  961 |   for(int i=0; i < gene2transcripts.size() * trace_length; i++) mu_trace_gene[i]=0;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1098:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1098 |   for(unsigned t=0; t < n; t++) gofs << indexSid[t] << " ";
      |                     ~~^~~
mmseq.cpp:1112:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1112 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1136:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1136 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1144:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1144 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1149:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1149 |   for(int i=0;i < identical_transcripts.size(); i++) {
      |               ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1156:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1156 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1161:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1161 |   for(int i=0;i < gene2transcripts.size(); i++) {
      |               ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1168:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1168 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1179:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1179 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1189:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1189 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1208:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1208 |     for(int t=0; t < identical_transcripts.size() ; t++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1212:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1212 |     for(int t=0; t < gene2transcripts.size(); t++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1226:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1226 |   for(int i=0; i < identical_transcripts.size() ; i++) meanmu_identical[i] /= trace_length;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1227:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1227 |   for(int i=0; i < gene2transcripts.size(); i++) meanmu_gene[i]/= trace_length;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1330:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1330 |   for(int t=0; t < identical_transcripts.size(); t++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1349:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1349 |   for(int g=0; g < gene2transcripts.size(); g++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1473:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1473 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1475:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1475 |     if(i==percentiles.size()-1) {
      |        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1482:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1482 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1484:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1484 |     if(i==percentiles.size()-1) {
      |        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1506:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1506 |       for(int i=0; i < percentiles.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1508:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1508 |         if(i==percentiles.size()-1) {
      |            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1514:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1514 |       for(int i=0; i < percentiles.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1516:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1516 |         if(i==percentiles.size()-1) {
      |            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1536:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1536 |       for(int i=0; i < percentiles.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1538:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1538 |         if(i==percentiles.size()-1) {
      |            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1544:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1544 |       for(int i=0; i < percentiles.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1546:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1546 |         if(i==percentiles.size()-1) {
      |            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1560:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1560 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1562:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1562 |     if(i==percentiles.size()-1) {
      |        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1582:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1582 |         for(int i=0; i < percentiles.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1584:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1584 |           if(i==percentiles.size()-1) {
      |              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1599:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1599 |         for(int i=0; i < percentiles.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1601:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1601 |           if(i==percentiles.size()-1) {
      |              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1619:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1619 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1621:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1621 |     if(i==percentiles.size()-1) {
      |        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1644:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1644 |         for(int i=0; i < percentiles.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1646:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1646 |           if(i==percentiles.size()-1) {
      |              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1656:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1656 |         for(int i=0; i < percentiles.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1658:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1658 |           if(i==percentiles.size()-1) {
      |              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:308:8: warning: unused variable ‘buf16384’ [-Wunused-variable]
  308 |   char buf16384[16384];
      |        ^~~~~~~~
mmseq.cpp:391:8: warning: variable ‘doublehit’ set but not used [-Wunused-but-set-variable]
  391 |   bool doublehit;
      |        ^~~~~~~~~
bam2hits.cpp: In function ‘void outputMergeHeaders(std::vector<FastaRecord>&, char, const char*, bool, HitsfileWriter&)’:
bam2hits.cpp:109:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  109 |   for(int i=0; i < sortedfastas.size()-1; i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:119:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  119 |       for(int j=0; j < curSet.size()-1; j++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:137:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  137 |   for(int j=0; j < curSet.size()-1; j++) {
      |                ~~^~~~~~~~~~~~~~~~~
bam2hits.cpp: In function ‘std::vector<Alignment> repetitiveTranscriptFilter(std::vector<Alignment>&, int)’:
bam2hits.cpp:218:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Alignment>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  218 |   for(int j=0; j < alns.size(); j++) {
      |                ~~^~~~~~~~~~~~~
bam2hits.cpp:219:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  219 |     if(i < torem.size() && j==torem[i]) {
      |        ~~^~~~~~~~~~~~~~
bam2hits.cpp: In function ‘int main(int, char**)’:
bam2hits.cpp:518:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  518 |         if(_B != tg[0].size()-2) {
      |            ~~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:520:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  520 |           if(_A == tg[0].size()-2) {
      |              ~~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:522:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  522 |             if(_A != tg[1].size()-2) {
      |                ~~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:558:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  558 |       for(int i=1; i < tokens2.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~
bam2hits.cpp:609:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  609 |     for(int i=0; i < fastas.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~
bam2hits.cpp:645:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  645 |     for(int i=0;i < fastas.size(); i++) transcriptCounts[i] /= (double)fastas[i].seq().size();
      |                 ~~^~~~~~~~~~~~~~~
bam2hits.cpp:659:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  659 |     for(int i=0; i < fastas.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~
bam2hits.cpp:662:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  662 |         for(int j =0; j < fastas[i].seq().size(); j++) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:663:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  663 |           int tag = (j <= MSEQ_BEFORE || j >= fastas[i].seq().size()-MSEQ_AFTER) ? -2 : 0;
      |                                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:791:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  791 |       for(int j=MSEQ_BEFORE + 1; j <= fastas[i].seq().length()-MSEQ_AFTER; j++) {
      |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:920:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  920 |     for(int j=1; j < frequencies.size()-WINDOWFORISIZEMODE + 1; j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:948:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  948 |     for(int i=0; i < testIsizes.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~
bam2hits.cpp:959:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  959 |     for(int i=0; i < heights.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~
bam2hits.cpp:997:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  997 |       for(int fl=1; fl <= (it->seq()).size(); fl++) {
      |                     ~~~^~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:1091:56: warning: comparing the result of pointer addition ‘(bam_aux_get(((const bam1_t*)line), ((const char*)"NM")) + ((sizetype)ait.__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >::operator->()->Alignment::NM()))’ and NULL [-Waddress]
 1091 |             ait->NM(ait->NM() + bam_aux_get(line,"NM") == NULL ? 0 : bam_aux2i(bam_aux_get(line,"NM")));
      |                                                        ^
bms.cpp: In member function ‘arma::Col<int> BMS::m2v(arma::Mat<double>)’:
bms.cpp:36:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   36 |   for(int i=0; i < P.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:37:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   37 |     for(int j=0; j < P.n_rows; j++) {
      |                  ~~^~~~~~~~~~
bms.cpp: In member function ‘std::vector<double> BMS::meanvar(arma::Col<double>)’:
bms.cpp:76:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   76 |   for(int i=0;i < v.n_elem; i++) {
      |               ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::print(bool)’:
bms.cpp:93:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   93 |   for(int feature=0; feature < y->n_rows; feature++) {
      |                      ~~~~~~~~^~~~~~~~~~~
bms.cpp:97:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   97 |       for(int i=0; i < M.n_cols; i++) {
      |                    ~~^~~~~~~~~~
bms.cpp:102:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  102 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::printtune(int)’:
bms.cpp:132:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  132 |   for(int feature=0; feature < y->n_rows; feature++) {
      |                      ~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_alpha()’:
bms.cpp:185:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  185 |     for(int j=0; j < y->n_rows; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_beta()’:
bms.cpp:253:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  253 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:255:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  255 |       for(int b=0; b < M.n_cols; b++) {
      |                    ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_eta()’:
bms.cpp:332:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  332 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:334:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  334 |       for(int c=0; c < P[model].n_cols; c++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_sigmasq()’:
bms.cpp:415:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  415 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_lambda()’:
bms.cpp:504:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  504 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:506:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  506 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_rho()’:
bms.cpp:559:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  559 |     for(int j=0; j < y->n_rows; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::copy_pseudo()’:
bms.cpp:582:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  582 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:585:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  585 |     for(int c=0; c < P[0].n_cols; c++) {
      |                  ~~^~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_alpha(int, int, bool)’:
bms.cpp:603:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  603 |     for(int j=0; j < y->n_cols; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:610:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  610 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_beta(int, int, bool)’:
bms.cpp:631:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  631 |     for(int j=0; j < y->n_cols; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:638:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  638 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  646 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  651 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_eta(int, int, bool)’:
bms.cpp:663:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  663 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:666:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  666 |       for(int i=0; i < y->n_cols; i++) {
      |                    ~~^~~~~~~~~~~
bms.cpp:673:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  673 |       for(int i=0; i < y->n_cols; i++) {
      |                    ~~^~~~~~~~~~~
bms.cpp:681:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  681 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:686:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  686 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_lambda(int, int, bool)’:
bms.cpp:699:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  699 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:704:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  704 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:711:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  711 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_sigmasq(int, int, bool, bool)’:
bms.cpp:729:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  729 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:740:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  740 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:751:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  751 |         for(int i=0; i < y->n_cols; i++) {
      |                      ~~^~~~~~~~~~~
bms.cpp:763:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  763 |         for(int i=0; i < y->n_cols; i++) {
      |                      ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_sigmasq_RW(int, int, bool, bool)’:
bms.cpp:877:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  877 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘double BMS::log_target_posterior(int, int)’:
bms.cpp:931:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  931 |   for(int i=0; i < y->n_cols; i++) {
      |                ~~^~~~~~~~~~~
bms.cpp:940:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  940 |     for(int j=0; j < M.n_cols; j++) {
      |                  ~~^~~~~~~~~~
bms.cpp:947:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  947 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘double BMS::log_target_pseudo(int, int)’:
bms.cpp:968:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  968 |     for(int l=0; l < M.n_cols; l++) {
      |                  ~~^~~~~~~~~~
bms.cpp:974:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  974 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::print_pseudo()’:
bms.cpp:1086:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1086 |     for(int l=0; l < M.n_cols; l++) {
      |                  ~~^~~~~~~~~~
bms.cpp:1089:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1089 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:1100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1100 |   for(int i=0; i < y->n_rows; i++) {
      |                ~~^~~~~~~~~~~
bms.cpp:1103:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1103 |       for(int l=0; l < M.n_cols; l++) {
      |                    ~~^~~~~~~~~~
bms.cpp:1106:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1106 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In constructor ‘BMS::BMS(const arma::Mat<double>*, const arma::Mat<double>&, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<int>, double, double, double, std::string, gsl_rng**, int, bool)’:
bms.cpp:1188:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1188 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:1192:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1192 |         if(C(i,model)+1 > _n.size()) {
      |            ~~~~~~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::initialise_streams(std::string)’:
bms.cpp:1348:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1348 |   for(int i=0; i < M.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:1354:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1354 |   for(int i=0; i < M.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:1360:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1360 |   for(int i=0; i < P[0].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1366:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1366 |   for(int i=0; i < P[1].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1372:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1372 |   for(int i=0; i < P[0].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1378:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1378 |   for(int i=0; i < P[1].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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 -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -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++/13/algorithm:61,
                 from mmdiff.cpp:31:
/usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here
 4581 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
      |     ^~~~~~~~~~~~~~
mmdiff.cpp:260:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  260 |     for(int j=0; j < y.n_cols; j++) {
      |                  ~~^~~~~~~~~~
mmdiff.cpp: In function ‘void parse_matrices(std::string, arma::Mat<double>&, arma::Mat<double>&, arma::Mat<double>&, arma::Mat<int>&, int)’:
mmdiff.cpp:310:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  310 |     for(int t=0; t < tokens.size(); t++) {
      |                  ~~^~~~~~~~~~~~~~~
mmdiff.cpp: In function ‘int main(int, char**)’:
mmdiff.cpp:420:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  420 |       for(int i=0; i < arguments.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:431:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  431 |       for(int i=0; i < arguments.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:439:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  439 |       while(ss < arguments.size()) {
      |             ~~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:451:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  451 |       if(ss != arguments.size()) {
      |          ~~~^~~~~~~~~~~~~~~~~~~
mmdiff.cpp:578:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  578 |   for(int i=0; i < arguments.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:640:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  640 |     for(int i=0; i < simple_de.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:759:17: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  759 |     if(inburnin && iter == OUTLEN/10 || !inburnin && iter==tuneiters) {
      |        ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:764:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  764 |     for(int feature=0; feature < features.size(); feature++) {
      |                        ~~~~~~~~^~~~~~~~~~~~~~~~~
mmdiff.cpp:837:17: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  837 |     if(inburnin && iter % subsample_burnin ==0 || !inburnin && iter >= tuneiters && (iter - tuneiters) % subsample_iter == 0) {
      |        ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:886:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  886 |       for(int l=0; l < M.n_cols; l++) {
      |                    ~~^~~~~~~~~~
mmdiff.cpp:898:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  898 |   for(int f=0; f < samplenames.size(); f++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:902:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  902 |       found2 = found2==string::npos ? -1 : found2;
      |                ~~~~~~^~~~~~~~~~~~~~
mmdiff.cpp:907:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  907 |   for(int f=0; f < samplenames.size(); f++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:909:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  909 |     if(f < samplenames.size()-1) cout << "\t";
      |        ~~^~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:914:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  914 |   for(int feature=0; feature < features.size(); feature++) {
      |                      ~~~~~~~~^~~~~~~~~~~~~~~~~
mmdiff.cpp:926:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  926 |         for(int l=0; l < M.n_cols; l++) {
      |                      ~~^~~~~~~~~~
mmdiff.cpp:936:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  936 |     for(int f=0; f < samplenames.size(); f++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:939:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  939 |     for(int f=0; f < samplenames.size(); f++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:941:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  941 |       if(f < samplenames.size()-1) cout << "\t";
      |          ~~^~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:951:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  951 |       for(int feature=0; feature < features.size(); feature++) {
      |                          ~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/bin/ld: /tmp/ccJrXIg6.ltrans0.ltrans.o: in function `main':
/builddir/build/BUILD/mmseq-1.0.11/src/bam2hits.cpp:653:(.text.startup+0x2510): 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.Xk00nC
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64
++ dirname /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,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/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64
+ mkdir -p /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/bin
+ install -p -m 0755 bin/bam2hits /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/bin
+ install -p -m 0755 bin/extract_transcripts /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/bin
+ install -p -m 0755 bin/hitstools /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/bin
+ install -p -m 0755 bin/mmcollapse /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/bin
+ install -p -m 0755 bin/mmdiff /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/bin
+ install -p -m 0755 bin/mmseq /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/bin
+ install -p -m 0755 bin/offsetGTF /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/bin
+ install -p -m 0755 bin/t2g_hits /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/bin
+ install -p -m 0755 bin/fastagrep.sh bin/mouse_strain_transcriptome.sh bin/usage.sh /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/bin
+ install -p -m 0755 bin/filterGTF.rb bin/haploref.rb bin/testregexp.rb /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/bin
+ install -p -m 0755 bin/ensembl_gtf_to_gff.pl /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/bin
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 1.0.11-16.fc40 --unique-debug-suffix -1.0.11-16.fc40.aarch64 --unique-debug-src-base mmseq-1.0.11-16.fc40.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/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-1.0.11-16.fc40.aarch64
542 blocks
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/ensembl_gtf_to_gff.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/testregexp.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/bin/haploref.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/bin/filterGTF.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/bin/usage.sh from /bin/bash to #!/usr/bin/bash
mangling shebang in /usr/bin/mouse_strain_transcriptome.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/fastagrep.sh from /bin/bash to #!/usr/bin/bash
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.D1ZKty
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,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-1.0.11-16.fc40.aarch64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.pim9Ee
+ umask 022
+ cd /builddir/build/BUILD
+ cd mmseq-1.0.11
+ DOCDIR=/builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/share/doc/mmseq
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/share/doc/mmseq
+ cp -pr /builddir/build/BUILD/mmseq-1.0.11/README.md /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/share/doc/mmseq
+ cp -pr /builddir/build/BUILD/mmseq-1.0.11/COPYING /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/share/doc/mmseq
+ cp -pr /builddir/build/BUILD/mmseq-1.0.11/doc /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64/usr/share/doc/mmseq
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: mmseq = 1.0.11-16.fc40 mmseq(aarch-64) = 1.0.11-16.fc40
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 ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libboost_iostreams.so.1.83.0()(64bit) libboost_regex.so.1.83.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(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) 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.27()(64bit) libgslcblas.so.0()(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(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-1.0.11-16.fc40.aarch64
Provides: mmseq-debugsource = 1.0.11-16.fc40 mmseq-debugsource(aarch-64) = 1.0.11-16.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: mmseq-debuginfo-1.0.11-16.fc40.aarch64
Provides: debuginfo(build-id) = 0bb0e03f0bbdfbe99406e3a2ccf8e4ec96f1a938 debuginfo(build-id) = 0f62ba05c1591b4c46eccfc4815bcd05b14cc823 debuginfo(build-id) = 11624eecac83022c2c8d5ab96324ccd5160b08b5 debuginfo(build-id) = 14be62aadcf2a8bd8354d51711c9ace49dab2ec1 debuginfo(build-id) = 2dbc89dc60168760f8943bea794808f6ba53c339 debuginfo(build-id) = 61567784c97cf886ea591bc71e2b6f2aef19437f debuginfo(build-id) = 777d691521209fb145188dcd0240e10ef0a25e27 debuginfo(build-id) = 7e429f6d24c11de57c926fd9c4db31861be02ff0 mmseq-debuginfo = 1.0.11-16.fc40 mmseq-debuginfo(aarch-64) = 1.0.11-16.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: mmseq-debugsource(aarch-64) = 1.0.11-16.fc40
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64
Wrote: /builddir/build/RPMS/mmseq-debugsource-1.0.11-16.fc40.aarch64.rpm
Wrote: /builddir/build/RPMS/mmseq-1.0.11-16.fc40.aarch64.rpm
Wrote: /builddir/build/RPMS/mmseq-debuginfo-1.0.11-16.fc40.aarch64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.5LcoQ4
+ umask 022
+ cd /builddir/build/BUILD
+ cd mmseq-1.0.11
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.aarch64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.jnrobv
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf /builddir/build/BUILD/mmseq-1.0.11-SPECPARTS
+ rm -rf mmseq-1.0.11 mmseq-1.0.11.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0

RPM build warnings:
    %patchN is deprecated (1 usages found), use %patch N (or %patch -P N)
Finish: rpmbuild mmseq-1.0.11-16.fc40.src.rpm
Finish: build phase for mmseq-1.0.11-16.fc40.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-aarch64-1702411319.400365/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-aarch64-1702411319.400365/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-aarch64-1702411319.400365/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/mmseq-1.0.11-16.fc40.src.rpm) Config(child) 1 minutes 6 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-debuginfo",
            "epoch": null,
            "version": "1.0.11",
            "release": "16.fc40",
            "arch": "aarch64"
        },
        {
            "name": "mmseq",
            "epoch": null,
            "version": "1.0.11",
            "release": "16.fc40",
            "arch": "src"
        },
        {
            "name": "mmseq-debugsource",
            "epoch": null,
            "version": "1.0.11",
            "release": "16.fc40",
            "arch": "aarch64"
        },
        {
            "name": "mmseq",
            "epoch": null,
            "version": "1.0.11",
            "release": "16.fc40",
            "arch": "aarch64"
        }
    ]
}
RPMResults finished