Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c119' (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-i386 --chroot fedora-rawhide-i386


Version: 0.70
PID: 16045
Logging PID: 16046
Task:
{'appstream': False,
 'background': True,
 'build_id': 6745622,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-i386',
 '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-i386/',
            '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-i386',
 '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-s3qnrter/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-s3qnrter/mmseq', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-s3qnrter/mmseq'...

Running: git checkout 2ed9d1e86a2a9ad4b2b3dea57cbe20a8b80d3205 --

cmd: ['git', 'checkout', '2ed9d1e86a2a9ad4b2b3dea57cbe20a8b80d3205', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-s3qnrter/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

/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-s3qnrter/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
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 2781k  100 2781k    0     0  23.3M      0 --:--:-- --:--:-- --:--:-- 23.2M
INFO: Reading stdout from command: md5sum 1.0.11.zip

Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-s3qnrter/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-s3qnrter/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1702420631.229914 -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-s3qnrter/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-s3qnrter/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1702420631.229914 -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-s3qnrter/mmseq/mmseq.spec)  Config(fedora-rawhide-i686)
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-i686-bootstrap-1702420631.229914/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-i686-bootstrap-1702420631.229914/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/ef7f879f9a7c8f3b179a505bc57c531f411bc8d830c8c86540e47c3fe4f37c04/merged
INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/ef7f879f9a7c8f3b179a505bc57c531f411bc8d830c8c86540e47c3fe4f37c04/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                                 5.0 MB/s | 1.6 MB     00:00    
local                                            57 MB/s |  71 MB     00:01    
Last metadata expiration check: 0:00:01 ago on Tue Dec 12 22:37:14 2023.
Package python3-dnf-4.18.2-1.fc40.noarch is already installed.
Dependencies resolved.
================================================================================
 Package                      Arch       Version                Repo       Size
================================================================================
Installing:
 python3-dnf-plugins-core     noarch     4.4.4-1.fc40           local     302 k
Installing dependencies:
 dbus-libs                    x86_64     1:1.14.10-1.fc40       local     155 k
 python3-dateutil             noarch     1:2.8.2-11.fc40        local     345 k
 python3-dbus                 x86_64     1.3.2-4.fc39           local     146 k
 python3-distro               noarch     1.8.0-6.fc39           local      44 k
 python3-six                  noarch     1.16.0-12.fc39         local      41 k
 python3-systemd              x86_64     235-5.fc39             local     101 k

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

Total download size: 1.1 M
Installed size: 3.6 M
Downloading Packages:
(1/7): dbus-libs-1.14.10-1.fc40.x86_64.rpm      2.7 MB/s | 155 kB     00:00    
(2/7): python3-distro-1.8.0-6.fc39.noarch.rpm   4.7 MB/s |  44 kB     00:00    
(3/7): python3-dateutil-2.8.2-11.fc40.noarch.rp 4.2 MB/s | 345 kB     00:00    
(4/7): python3-dbus-1.3.2-4.fc39.x86_64.rpm     1.8 MB/s | 146 kB     00:00    
(5/7): python3-dnf-plugins-core-4.4.4-1.fc40.no  16 MB/s | 302 kB     00:00    
(6/7): python3-six-1.16.0-12.fc39.noarch.rpm    4.4 MB/s |  41 kB     00:00    
(7/7): python3-systemd-235-5.fc39.x86_64.rpm    8.7 MB/s | 101 kB     00:00    
--------------------------------------------------------------------------------
Total                                            12 MB/s | 1.1 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.x86_64                      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.x86_64                      5/7 
  Installing       : python3-dbus-1.3.2-4.fc39.x86_64                       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.x86_64                                             
  python3-dateutil-1:2.8.2-11.fc40.noarch                                       
  python3-dbus-1.3.2-4.fc39.x86_64                                              
  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.x86_64                                             

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-i686-1702420631.229914/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                                  38 kB/s | 1.5 kB     00:00    
Copr repository                                  13 MB/s | 1.6 MB     00:00    
local                                            78 kB/s | 3.8 kB     00:00    
local                                            61 MB/s |  60 MB     00:00    
Dependencies resolved.
================================================================================
 Package                       Arch   Version                       Repo   Size
================================================================================
Installing group/module packages:
 bash                          i686   5.2.21-2.fc40                 local 1.8 M
 bzip2                         i686   1.0.8-16.fc39                 local  53 k
 coreutils                     i686   9.4-1.fc40                    local 1.2 M
 cpio                          i686   2.14-5.fc40                   local 278 k
 diffutils                     i686   3.10-3.fc39                   local 394 k
 fedora-release                noarch 40-0.20                       local 9.3 k
 findutils                     i686   1:4.9.0-6.fc40                local 492 k
 gawk                          i686   5.2.2-2.fc39                  local 1.0 M
 glibc-minimal-langpack        i686   2.38.9000-26.fc40             local  85 k
 grep                          i686   3.11-5.fc40                   local 294 k
 gzip                          i686   1.12-6.fc39                   local 158 k
 info                          i686   7.1-1.fc40                    local 187 k
 patch                         i686   2.7.6-22.fc39                 local 138 k
 redhat-rpm-config             noarch 271-1.fc40                    local  74 k
 rpm-build                     i686   4.19.1-1.fc40                 local  72 k
 sed                           i686   4.8-14.fc39                   local 300 k
 shadow-utils                  i686   2:4.14.0-2.fc40               local 1.2 M
 tar                           i686   2:1.35-2.fc40                 local 864 k
 unzip                         i686   6.0-62.fc39                   local 180 k
 util-linux                    i686   2.39.2-1.fc40                 local 1.2 M
 which                         i686   2.21-40.fc39                  local  42 k
 xz                            i686   5.4.5-1.fc40                  local 535 k
Installing dependencies:
 alternatives                  i686   1.25-1.fc39                   local  39 k
 ansible-srpm-macros           noarch 1-11.fc39                     local  21 k
 audit-libs                    i686   3.1.2-5.fc40                  local 125 k
 authselect                    i686   1.4.3-1.fc40                  local 145 k
 authselect-libs               i686   1.4.3-1.fc40                  local 237 k
 basesystem                    noarch 11-18.fc39                    local 7.2 k
 binutils                      i686   2.41-16.fc40                  local 5.9 M
 binutils-gold                 i686   2.41-16.fc40                  local 863 k
 bzip2-libs                    i686   1.0.8-16.fc39                 local  41 k
 ca-certificates               noarch 2023.2.62_v7.0.401-4.fc40     local 863 k
 coreutils-common              i686   9.4-1.fc40                    local 2.1 M
 cracklib                      i686   2.9.11-2.fc39                 local  83 k
 crypto-policies               noarch 20231204-1.git1e3a2e4.fc40    local  69 k
 curl                          i686   8.5.0-1.fc40                  local 375 k
 cyrus-sasl-lib                i686   2.1.28-11.fc39                local 857 k
 debugedit                     i686   5.0-12.fc40                   local  80 k
 dwz                           i686   0.15-3.fc39                   local 139 k
 ed                            i686   1.19-4.fc39                   local  78 k
 efi-srpm-macros               noarch 5-9.fc39                      local  22 k
 elfutils                      i686   0.190-4.fc40                  local 568 k
 elfutils-debuginfod-client    i686   0.190-4.fc40                  local  38 k
 elfutils-default-yama-scope   noarch 0.190-4.fc40                  local  13 k
 elfutils-libelf               i686   0.190-4.fc40                  local 201 k
 elfutils-libs                 i686   0.190-4.fc40                  local 290 k
 fedora-gpg-keys               noarch 40-0.2                        local 119 k
 fedora-release-common         noarch 40-0.20                       local  20 k
 fedora-release-identity-basic noarch 40-0.20                       local  10 k
 fedora-repos                  noarch 40-0.2                        local 9.3 k
 fedora-repos-rawhide          noarch 40-0.2                        local 8.9 k
 file                          i686   5.45-1.fc40                   local  49 k
 file-libs                     i686   5.45-1.fc40                   local 770 k
 filesystem                    i686   3.18-6.fc39                   local 1.1 M
 fonts-srpm-macros             noarch 1:2.0.5-12.fc39               local  26 k
 forge-srpm-macros             noarch 0.2.0-1.fc40                  local  18 k
 fpc-srpm-macros               noarch 1.3-8.fc39                    local 7.4 k
 gdb-minimal                   i686   14.1-1.fc40                   local 4.6 M
 gdbm                          i686   1:1.23-4.fc39                 local 150 k
 gdbm-libs                     i686   1:1.23-4.fc39                 local  60 k
 ghc-srpm-macros               noarch 1.6.1-3.fc40                  local 8.1 k
 glibc                         i686   2.38.9000-26.fc40             local 2.0 M
 glibc-common                  i686   2.38.9000-26.fc40             local 374 k
 glibc-gconv-extra             i686   2.38.9000-26.fc40             local 1.7 M
 gmp                           i686   1:6.2.1-5.fc39                local 306 k
 gnat-srpm-macros              noarch 6-3.fc39                      local 8.8 k
 go-srpm-macros                noarch 3.3.1-1.fc40                  local  28 k
 jansson                       i686   2.13.1-7.fc39                 local  46 k
 kernel-srpm-macros            noarch 1.0-20.fc39                   local  10 k
 keyutils-libs                 i686   1.6.1-7.fc39                  local  32 k
 krb5-libs                     i686   1.21.2-2.fc40                 local 804 k
 libacl                        i686   2.3.1-11.fc40                 local  25 k
 libarchive                    i686   3.7.2-1.fc40                  local 450 k
 libattr                       i686   2.5.1-9.fc40                  local  18 k
 libblkid                      i686   2.39.2-1.fc40                 local 127 k
 libbrotli                     i686   1.1.0-1.fc40                  local 340 k
 libcap                        i686   2.69-1.fc40                   local  84 k
 libcap-ng                     i686   0.8.3-8.fc40                  local  33 k
 libcom_err                    i686   1.47.0-2.fc39                 local  26 k
 libcurl                       i686   8.5.0-1.fc40                  local 372 k
 libeconf                      i686   0.5.2-1.fc40                  local  32 k
 libevent                      i686   2.1.12-9.fc39                 local 277 k
 libfdisk                      i686   2.39.2-1.fc40                 local 175 k
 libffi                        i686   3.4.4-4.fc39                  local  38 k
 libgcc                        i686   13.2.1-6.fc40                 local 121 k
 libgomp                       i686   13.2.1-6.fc40                 local 324 k
 libidn2                       i686   2.3.4-3.fc39                  local 111 k
 libmount                      i686   2.39.2-1.fc40                 local 161 k
 libnghttp2                    i686   1.58.0-1.fc40                 local  82 k
 libnsl2                       i686   2.0.0-6.fc39                  local  31 k
 libpkgconf                    i686   1.9.5-2.fc39                  local  41 k
 libpsl                        i686   0.21.2-4.fc39                 local  63 k
 libpwquality                  i686   1.4.5-6.fc39                  local 109 k
 libselinux                    i686   3.6-0.rc2.1.fc40              local  93 k
 libsemanage                   i686   3.6-0.rc2.1.fc40              local 125 k
 libsepol                      i686   3.6-0.rc2.1.fc40              local 352 k
 libsigsegv                    i686   2.14-5.fc39                   local  27 k
 libsmartcols                  i686   2.39.2-1.fc40                 local  69 k
 libssh                        i686   0.10.5-2.fc39                 local 226 k
 libssh-config                 noarch 0.10.5-2.fc39                 local 9.2 k
 libstdc++                     i686   13.2.1-6.fc40                 local 931 k
 libtasn1                      i686   4.19.0-3.fc39                 local  75 k
 libtirpc                      i686   1.3.4-0.fc40                  local 101 k
 libunistring                  i686   1.1-5.fc40                    local 551 k
 libutempter                   i686   1.2.1-10.fc39                 local  27 k
 libuuid                       i686   2.39.2-1.fc40                 local  29 k
 libverto                      i686   0.3.2-6.fc39                  local  21 k
 libxcrypt                     i686   4.4.36-2.fc39                 local 123 k
 libxml2                       i686   2.12.3-1.fc40                 local 729 k
 libzstd                       i686   1.5.5-4.fc39                  local 290 k
 lua-libs                      i686   5.4.6-3.fc39                  local 149 k
 lua-srpm-macros               noarch 1-9.fc39                      local 8.6 k
 lz4-libs                      i686   1.9.4-4.fc39                  local  70 k
 mpfr                          i686   4.2.1-1.fc40                  local 380 k
 ncurses-base                  noarch 6.4-8.20231001.fc40           local  63 k
 ncurses-libs                  i686   6.4-8.20231001.fc40           local 359 k
 ocaml-srpm-macros             noarch 9-1.fc40                      local 9.0 k
 openblas-srpm-macros          noarch 2-14.fc39                     local 7.5 k
 openldap                      i686   2.6.6-1.fc39                  local 273 k
 openssl-libs                  i686   1:3.1.4-1.fc40                local 2.1 M
 p11-kit                       i686   0.25.3-1.fc40                 local 490 k
 p11-kit-trust                 i686   0.25.3-1.fc40                 local 140 k
 package-notes-srpm-macros     noarch 0.5-9.fc39                    local  11 k
 pam                           i686   1.5.3-8.fc40                  local 528 k
 pam-libs                      i686   1.5.3-8.fc40                  local  60 k
 pcre2                         i686   10.42-2.fc40                  local 231 k
 pcre2-syntax                  noarch 10.42-2.fc40                  local 143 k
 perl-srpm-macros              noarch 1-51.fc39                     local 8.0 k
 pkgconf                       i686   1.9.5-2.fc39                  local  43 k
 pkgconf-m4                    noarch 1.9.5-2.fc39                  local  14 k
 pkgconf-pkg-config            i686   1.9.5-2.fc39                  local 9.6 k
 popt                          i686   1.19-3.fc39                   local  62 k
 publicsuffix-list-dafsa       noarch 20230812-1.fc40               local  57 k
 pyproject-srpm-macros         noarch 1.10.0-1.fc40                 local  14 k
 python-srpm-macros            noarch 3.12-5.fc40                   local  25 k
 qt5-srpm-macros               noarch 5.15.11-1.fc40                local 8.3 k
 qt6-srpm-macros               noarch 6.6.1-1.fc40                  local 8.6 k
 readline                      i686   8.2-4.fc39                    local 218 k
 rpm                           i686   4.19.1-1.fc40                 local 507 k
 rpm-build-libs                i686   4.19.1-1.fc40                 local 102 k
 rpm-libs                      i686   4.19.1-1.fc40                 local 341 k
 rpm-sequoia                   i686   1.5.0-2.fc40                  local 945 k
 rust-srpm-macros              noarch 25.2-2.fc40                   local  13 k
 setup                         noarch 2.14.5-1.fc40                 local 148 k
 sqlite-libs                   i686   3.44.2-1.fc40                 local 733 k
 systemd-libs                  i686   255-1.fc40                    local 743 k
 util-linux-core               i686   2.39.2-1.fc40                 local 491 k
 xxhash-libs                   i686   0.8.2-1.fc39                  local  49 k
 xz-libs                       i686   5.4.5-1.fc40                  local 118 k
 zip                           i686   3.0-39.fc40                   local 267 k
 zlib                          i686   1.2.13-5.fc40                 local  93 k
 zstd                          i686   1.5.5-4.fc39                  local 451 k
Installing Groups:
 build                                                                         

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

Total size: 53 M
Installed size: 175 M
Downloading Packages:
[SKIPPED] alternatives-1.25-1.fc39.i686.rpm: Already downloaded                
[SKIPPED] ansible-srpm-macros-1-11.fc39.noarch.rpm: Already downloaded         
[SKIPPED] audit-libs-3.1.2-5.fc40.i686.rpm: Already downloaded                 
[SKIPPED] authselect-1.4.3-1.fc40.i686.rpm: Already downloaded                 
[SKIPPED] authselect-libs-1.4.3-1.fc40.i686.rpm: Already downloaded            
[SKIPPED] basesystem-11-18.fc39.noarch.rpm: Already downloaded                 
[SKIPPED] bash-5.2.21-2.fc40.i686.rpm: Already downloaded                      
[SKIPPED] binutils-2.41-16.fc40.i686.rpm: Already downloaded                   
[SKIPPED] binutils-gold-2.41-16.fc40.i686.rpm: Already downloaded              
[SKIPPED] bzip2-1.0.8-16.fc39.i686.rpm: Already downloaded                     
[SKIPPED] bzip2-libs-1.0.8-16.fc39.i686.rpm: Already downloaded                
[SKIPPED] ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch.rpm: Already downloaded
[SKIPPED] coreutils-9.4-1.fc40.i686.rpm: Already downloaded                    
[SKIPPED] coreutils-common-9.4-1.fc40.i686.rpm: Already downloaded             
[SKIPPED] cpio-2.14-5.fc40.i686.rpm: Already downloaded                        
[SKIPPED] cracklib-2.9.11-2.fc39.i686.rpm: Already downloaded                  
[SKIPPED] crypto-policies-20231204-1.git1e3a2e4.fc40.noarch.rpm: Already downloaded
[SKIPPED] curl-8.5.0-1.fc40.i686.rpm: Already downloaded                       
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Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.18-6.fc39.i686                            1/1 
  Preparing        :                                                        1/1 
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  Installing       : setup-2.14.5-1.fc40.noarch                           8/152 
warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.14.5-1.fc40.noarch                           8/152 
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  Installing       : sqlite-libs-3.44.2-1.fc40.i686                      93/152 
  Installing       : ed-1.19-4.fc39.i686                                 94/152 
  Installing       : patch-2.7.6-22.fc39.i686                            95/152 
  Installing       : cpio-2.14-5.fc40.i686                               96/152 
  Installing       : diffutils-3.10-3.fc39.i686                          97/152 
  Installing       : keyutils-libs-1.6.1-7.fc39.i686                     98/152 
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  Installing       : authselect-1.4.3-1.fc40.i686                       110/152 
  Installing       : libarchive-3.7.2-1.fc40.i686                       111/152 
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  Installing       : openldap-2.6.6-1.fc39.i686                         113/152 
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  Installing       : rpm-libs-4.19.1-1.fc40.i686                        115/152 
  Installing       : libgomp-13.2.1-6.fc40.i686                         116/152 
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  Installing       : libpkgconf-1.9.5-2.fc39.i686                       118/152 
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  Installing       : krb5-libs-1.21.2-2.fc40.i686                       124/152 
  Installing       : libtirpc-1.3.4-0.fc40.i686                         125/152 
  Installing       : libnsl2-2.0.0-6.fc39.i686                          126/152 
  Installing       : pam-1.5.3-8.fc40.i686                              127/152 
  Installing       : libssh-0.10.5-2.fc39.i686                          128/152 
  Installing       : libcurl-8.5.0-1.fc40.i686                          129/152 
  Installing       : elfutils-libs-0.190-4.fc40.i686                    130/152 
  Installing       : elfutils-debuginfod-client-0.190-4.fc40.i686       131/152 
  Installing       : binutils-gold-2.41-16.fc40.i686                    132/152 
  Running scriptlet: binutils-gold-2.41-16.fc40.i686                    132/152 
  Installing       : binutils-2.41-16.fc40.i686                         133/152 
  Running scriptlet: binutils-2.41-16.fc40.i686                         133/152 
  Installing       : elfutils-0.190-4.fc40.i686                         134/152 
  Installing       : rpm-build-libs-4.19.1-1.fc40.i686                  135/152 
  Installing       : curl-8.5.0-1.fc40.i686                             136/152 
  Running scriptlet: rpm-4.19.1-1.fc40.i686                             137/152 
  Installing       : rpm-4.19.1-1.fc40.i686                             137/152 
  Installing       : efi-srpm-macros-5-9.fc39.noarch                    138/152 
  Installing       : lua-srpm-macros-1-9.fc39.noarch                    139/152 
  Installing       : xxhash-libs-0.8.2-1.fc39.i686                      140/152 
  Installing       : gdb-minimal-14.1-1.fc40.i686                       141/152 
  Installing       : debugedit-5.0-12.fc40.i686                         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-4.19.1-1.fc40.i686                       148/152 
  Installing       : pyproject-srpm-macros-1.10.0-1.fc40.noarch         149/152 
  Installing       : util-linux-2.39.2-1.fc40.i686                      150/152 
  Installing       : which-2.21-40.fc39.i686                            151/152 
  Installing       : info-7.1-1.fc40.i686                               152/152 
  Running scriptlet: filesystem-3.18-6.fc39.i686                        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.i686                  152/152 
  Running scriptlet: rpm-4.19.1-1.fc40.i686                             152/152 
  Running scriptlet: info-7.1-1.fc40.i686                               152/152 

Installed:
  alternatives-1.25-1.fc39.i686                                                 
  ansible-srpm-macros-1-11.fc39.noarch                                          
  audit-libs-3.1.2-5.fc40.i686                                                  
  authselect-1.4.3-1.fc40.i686                                                  
  authselect-libs-1.4.3-1.fc40.i686                                             
  basesystem-11-18.fc39.noarch                                                  
  bash-5.2.21-2.fc40.i686                                                       
  binutils-2.41-16.fc40.i686                                                    
  binutils-gold-2.41-16.fc40.i686                                               
  bzip2-1.0.8-16.fc39.i686                                                      
  bzip2-libs-1.0.8-16.fc39.i686                                                 
  ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch                              
  coreutils-9.4-1.fc40.i686                                                     
  coreutils-common-9.4-1.fc40.i686                                              
  cpio-2.14-5.fc40.i686                                                         
  cracklib-2.9.11-2.fc39.i686                                                   
  crypto-policies-20231204-1.git1e3a2e4.fc40.noarch                             
  curl-8.5.0-1.fc40.i686                                                        
  cyrus-sasl-lib-2.1.28-11.fc39.i686                                            
  debugedit-5.0-12.fc40.i686                                                    
  diffutils-3.10-3.fc39.i686                                                    
  dwz-0.15-3.fc39.i686                                                          
  ed-1.19-4.fc39.i686                                                           
  efi-srpm-macros-5-9.fc39.noarch                                               
  elfutils-0.190-4.fc40.i686                                                    
  elfutils-debuginfod-client-0.190-4.fc40.i686                                  
  elfutils-default-yama-scope-0.190-4.fc40.noarch                               
  elfutils-libelf-0.190-4.fc40.i686                                             
  elfutils-libs-0.190-4.fc40.i686                                               
  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.i686                                                         
  file-libs-5.45-1.fc40.i686                                                    
  filesystem-3.18-6.fc39.i686                                                   
  findutils-1:4.9.0-6.fc40.i686                                                 
  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.i686                                                        
  gdb-minimal-14.1-1.fc40.i686                                                  
  gdbm-1:1.23-4.fc39.i686                                                       
  gdbm-libs-1:1.23-4.fc39.i686                                                  
  ghc-srpm-macros-1.6.1-3.fc40.noarch                                           
  glibc-2.38.9000-26.fc40.i686                                                  
  glibc-common-2.38.9000-26.fc40.i686                                           
  glibc-gconv-extra-2.38.9000-26.fc40.i686                                      
  glibc-minimal-langpack-2.38.9000-26.fc40.i686                                 
  gmp-1:6.2.1-5.fc39.i686                                                       
  gnat-srpm-macros-6-3.fc39.noarch                                              
  go-srpm-macros-3.3.1-1.fc40.noarch                                            
  grep-3.11-5.fc40.i686                                                         
  gzip-1.12-6.fc39.i686                                                         
  info-7.1-1.fc40.i686                                                          
  jansson-2.13.1-7.fc39.i686                                                    
  kernel-srpm-macros-1.0-20.fc39.noarch                                         
  keyutils-libs-1.6.1-7.fc39.i686                                               
  krb5-libs-1.21.2-2.fc40.i686                                                  
  libacl-2.3.1-11.fc40.i686                                                     
  libarchive-3.7.2-1.fc40.i686                                                  
  libattr-2.5.1-9.fc40.i686                                                     
  libblkid-2.39.2-1.fc40.i686                                                   
  libbrotli-1.1.0-1.fc40.i686                                                   
  libcap-2.69-1.fc40.i686                                                       
  libcap-ng-0.8.3-8.fc40.i686                                                   
  libcom_err-1.47.0-2.fc39.i686                                                 
  libcurl-8.5.0-1.fc40.i686                                                     
  libeconf-0.5.2-1.fc40.i686                                                    
  libevent-2.1.12-9.fc39.i686                                                   
  libfdisk-2.39.2-1.fc40.i686                                                   
  libffi-3.4.4-4.fc39.i686                                                      
  libgcc-13.2.1-6.fc40.i686                                                     
  libgomp-13.2.1-6.fc40.i686                                                    
  libidn2-2.3.4-3.fc39.i686                                                     
  libmount-2.39.2-1.fc40.i686                                                   
  libnghttp2-1.58.0-1.fc40.i686                                                 
  libnsl2-2.0.0-6.fc39.i686                                                     
  libpkgconf-1.9.5-2.fc39.i686                                                  
  libpsl-0.21.2-4.fc39.i686                                                     
  libpwquality-1.4.5-6.fc39.i686                                                
  libselinux-3.6-0.rc2.1.fc40.i686                                              
  libsemanage-3.6-0.rc2.1.fc40.i686                                             
  libsepol-3.6-0.rc2.1.fc40.i686                                                
  libsigsegv-2.14-5.fc39.i686                                                   
  libsmartcols-2.39.2-1.fc40.i686                                               
  libssh-0.10.5-2.fc39.i686                                                     
  libssh-config-0.10.5-2.fc39.noarch                                            
  libstdc++-13.2.1-6.fc40.i686                                                  
  libtasn1-4.19.0-3.fc39.i686                                                   
  libtirpc-1.3.4-0.fc40.i686                                                    
  libunistring-1.1-5.fc40.i686                                                  
  libutempter-1.2.1-10.fc39.i686                                                
  libuuid-2.39.2-1.fc40.i686                                                    
  libverto-0.3.2-6.fc39.i686                                                    
  libxcrypt-4.4.36-2.fc39.i686                                                  
  libxml2-2.12.3-1.fc40.i686                                                    
  libzstd-1.5.5-4.fc39.i686                                                     
  lua-libs-5.4.6-3.fc39.i686                                                    
  lua-srpm-macros-1-9.fc39.noarch                                               
  lz4-libs-1.9.4-4.fc39.i686                                                    
  mpfr-4.2.1-1.fc40.i686                                                        
  ncurses-base-6.4-8.20231001.fc40.noarch                                       
  ncurses-libs-6.4-8.20231001.fc40.i686                                         
  ocaml-srpm-macros-9-1.fc40.noarch                                             
  openblas-srpm-macros-2-14.fc39.noarch                                         
  openldap-2.6.6-1.fc39.i686                                                    
  openssl-libs-1:3.1.4-1.fc40.i686                                              
  p11-kit-0.25.3-1.fc40.i686                                                    
  p11-kit-trust-0.25.3-1.fc40.i686                                              
  package-notes-srpm-macros-0.5-9.fc39.noarch                                   
  pam-1.5.3-8.fc40.i686                                                         
  pam-libs-1.5.3-8.fc40.i686                                                    
  patch-2.7.6-22.fc39.i686                                                      
  pcre2-10.42-2.fc40.i686                                                       
  pcre2-syntax-10.42-2.fc40.noarch                                              
  perl-srpm-macros-1-51.fc39.noarch                                             
  pkgconf-1.9.5-2.fc39.i686                                                     
  pkgconf-m4-1.9.5-2.fc39.noarch                                                
  pkgconf-pkg-config-1.9.5-2.fc39.i686                                          
  popt-1.19-3.fc39.i686                                                         
  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.i686                                                      
  redhat-rpm-config-271-1.fc40.noarch                                           
  rpm-4.19.1-1.fc40.i686                                                        
  rpm-build-4.19.1-1.fc40.i686                                                  
  rpm-build-libs-4.19.1-1.fc40.i686                                             
  rpm-libs-4.19.1-1.fc40.i686                                                   
  rpm-sequoia-1.5.0-2.fc40.i686                                                 
  rust-srpm-macros-25.2-2.fc40.noarch                                           
  sed-4.8-14.fc39.i686                                                          
  setup-2.14.5-1.fc40.noarch                                                    
  shadow-utils-2:4.14.0-2.fc40.i686                                             
  sqlite-libs-3.44.2-1.fc40.i686                                                
  systemd-libs-255-1.fc40.i686                                                  
  tar-2:1.35-2.fc40.i686                                                        
  unzip-6.0-62.fc39.i686                                                        
  util-linux-2.39.2-1.fc40.i686                                                 
  util-linux-core-2.39.2-1.fc40.i686                                            
  which-2.21-40.fc39.i686                                                       
  xxhash-libs-0.8.2-1.fc39.i686                                                 
  xz-5.4.5-1.fc40.i686                                                          
  xz-libs-5.4.5-1.fc40.i686                                                     
  zip-3.0-39.fc40.i686                                                          
  zlib-1.2.13-5.fc40.i686                                                       
  zstd-1.5.5-4.fc39.i686                                                        

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.i686
ansible-srpm-macros-1-11.fc39.noarch
audit-libs-3.1.2-5.fc40.i686
authselect-1.4.3-1.fc40.i686
authselect-libs-1.4.3-1.fc40.i686
basesystem-11-18.fc39.noarch
bash-5.2.21-2.fc40.i686
binutils-2.41-16.fc40.i686
binutils-gold-2.41-16.fc40.i686
bzip2-1.0.8-16.fc39.i686
bzip2-libs-1.0.8-16.fc39.i686
ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch
coreutils-9.4-1.fc40.i686
coreutils-common-9.4-1.fc40.i686
cpio-2.14-5.fc40.i686
cracklib-2.9.11-2.fc39.i686
crypto-policies-20231204-1.git1e3a2e4.fc40.noarch
curl-8.5.0-1.fc40.i686
cyrus-sasl-lib-2.1.28-11.fc39.i686
debugedit-5.0-12.fc40.i686
diffutils-3.10-3.fc39.i686
dwz-0.15-3.fc39.i686
ed-1.19-4.fc39.i686
efi-srpm-macros-5-9.fc39.noarch
elfutils-0.190-4.fc40.i686
elfutils-debuginfod-client-0.190-4.fc40.i686
elfutils-default-yama-scope-0.190-4.fc40.noarch
elfutils-libelf-0.190-4.fc40.i686
elfutils-libs-0.190-4.fc40.i686
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.i686
file-libs-5.45-1.fc40.i686
filesystem-3.18-6.fc39.i686
findutils-4.9.0-6.fc40.i686
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.i686
gdb-minimal-14.1-1.fc40.i686
gdbm-1.23-4.fc39.i686
gdbm-libs-1.23-4.fc39.i686
ghc-srpm-macros-1.6.1-3.fc40.noarch
glibc-2.38.9000-26.fc40.i686
glibc-common-2.38.9000-26.fc40.i686
glibc-gconv-extra-2.38.9000-26.fc40.i686
glibc-minimal-langpack-2.38.9000-26.fc40.i686
gmp-6.2.1-5.fc39.i686
gnat-srpm-macros-6-3.fc39.noarch
go-srpm-macros-3.3.1-1.fc40.noarch
grep-3.11-5.fc40.i686
gzip-1.12-6.fc39.i686
info-7.1-1.fc40.i686
jansson-2.13.1-7.fc39.i686
kernel-srpm-macros-1.0-20.fc39.noarch
keyutils-libs-1.6.1-7.fc39.i686
krb5-libs-1.21.2-2.fc40.i686
libacl-2.3.1-11.fc40.i686
libarchive-3.7.2-1.fc40.i686
libattr-2.5.1-9.fc40.i686
libblkid-2.39.2-1.fc40.i686
libbrotli-1.1.0-1.fc40.i686
libcap-2.69-1.fc40.i686
libcap-ng-0.8.3-8.fc40.i686
libcom_err-1.47.0-2.fc39.i686
libcurl-8.5.0-1.fc40.i686
libeconf-0.5.2-1.fc40.i686
libevent-2.1.12-9.fc39.i686
libfdisk-2.39.2-1.fc40.i686
libffi-3.4.4-4.fc39.i686
libgcc-13.2.1-6.fc40.i686
libgomp-13.2.1-6.fc40.i686
libidn2-2.3.4-3.fc39.i686
libmount-2.39.2-1.fc40.i686
libnghttp2-1.58.0-1.fc40.i686
libnsl2-2.0.0-6.fc39.i686
libpkgconf-1.9.5-2.fc39.i686
libpsl-0.21.2-4.fc39.i686
libpwquality-1.4.5-6.fc39.i686
libselinux-3.6-0.rc2.1.fc40.i686
libsemanage-3.6-0.rc2.1.fc40.i686
libsepol-3.6-0.rc2.1.fc40.i686
libsigsegv-2.14-5.fc39.i686
libsmartcols-2.39.2-1.fc40.i686
libssh-0.10.5-2.fc39.i686
libssh-config-0.10.5-2.fc39.noarch
libstdc++-13.2.1-6.fc40.i686
libtasn1-4.19.0-3.fc39.i686
libtirpc-1.3.4-0.fc40.i686
libunistring-1.1-5.fc40.i686
libutempter-1.2.1-10.fc39.i686
libuuid-2.39.2-1.fc40.i686
libverto-0.3.2-6.fc39.i686
libxcrypt-4.4.36-2.fc39.i686
libxml2-2.12.3-1.fc40.i686
libzstd-1.5.5-4.fc39.i686
lua-libs-5.4.6-3.fc39.i686
lua-srpm-macros-1-9.fc39.noarch
lz4-libs-1.9.4-4.fc39.i686
mpfr-4.2.1-1.fc40.i686
ncurses-base-6.4-8.20231001.fc40.noarch
ncurses-libs-6.4-8.20231001.fc40.i686
ocaml-srpm-macros-9-1.fc40.noarch
openblas-srpm-macros-2-14.fc39.noarch
openldap-2.6.6-1.fc39.i686
openssl-libs-3.1.4-1.fc40.i686
p11-kit-0.25.3-1.fc40.i686
p11-kit-trust-0.25.3-1.fc40.i686
package-notes-srpm-macros-0.5-9.fc39.noarch
pam-1.5.3-8.fc40.i686
pam-libs-1.5.3-8.fc40.i686
patch-2.7.6-22.fc39.i686
pcre2-10.42-2.fc40.i686
pcre2-syntax-10.42-2.fc40.noarch
perl-srpm-macros-1-51.fc39.noarch
pkgconf-1.9.5-2.fc39.i686
pkgconf-m4-1.9.5-2.fc39.noarch
pkgconf-pkg-config-1.9.5-2.fc39.i686
popt-1.19-3.fc39.i686
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.i686
redhat-rpm-config-271-1.fc40.noarch
rpm-4.19.1-1.fc40.i686
rpm-build-4.19.1-1.fc40.i686
rpm-build-libs-4.19.1-1.fc40.i686
rpm-libs-4.19.1-1.fc40.i686
rpm-sequoia-1.5.0-2.fc40.i686
rust-srpm-macros-25.2-2.fc40.noarch
sed-4.8-14.fc39.i686
setup-2.14.5-1.fc40.noarch
shadow-utils-4.14.0-2.fc40.i686
sqlite-libs-3.44.2-1.fc40.i686
systemd-libs-255-1.fc40.i686
tar-1.35-2.fc40.i686
unzip-6.0-62.fc39.i686
util-linux-2.39.2-1.fc40.i686
util-linux-core-2.39.2-1.fc40.i686
which-2.21-40.fc39.i686
xxhash-libs-0.8.2-1.fc39.i686
xz-5.4.5-1.fc40.i686
xz-libs-5.4.5-1.fc40.i686
zip-3.0-39.fc40.i686
zlib-1.2.13-5.fc40.i686
zstd-1.5.5-4.fc39.i686
Start: buildsrpm
Start: rpmbuild -bs
warning: %patchN is deprecated (1 usages found), use %patch N (or %patch -P N)
Building target platforms: i686
Building for target i686
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-i686-1702420631.229914/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-i686-1702420631.229914/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-i686-1702420631.229914/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-s3qnrter/mmseq/mmseq.spec) Config(child) 0 minutes 56 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-i686)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-i686-bootstrap-1702420631.229914/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-i686-bootstrap-1702420631.229914/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-i686-1702420631.229914/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.x86_64
  rpm-sequoia-1.5.0-2.fc40.x86_64
  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: i686
Building for target i686
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                                  41 kB/s | 1.5 kB     00:00    
local                                            98 kB/s | 3.8 kB     00:00    
Dependencies resolved.
================================================================================
 Package                     Arch     Version                 Repository   Size
================================================================================
Installing:
 armadillo-devel             i686     10.8.2-5.fc39           local       2.1 M
 boost-devel                 i686     1.83.0-0.fc40           copr_base    12 M
 flexiblas-devel             i686     3.3.1-5.fc39            local       103 k
 gcc-c++                     i686     13.2.1-6.fc40           local        13 M
 gsl-devel                   i686     2.7.1-5.fc39            local       609 k
 htslib-devel                i686     1.15.1-3.fc39           local        99 k
 make                        i686     1:4.4.1-2.fc39          local       589 k
 perl-generators             noarch   1.16-3.fc39             local        16 k
 zlib-devel                  i686     1.2.13-5.fc40           local        44 k
Installing dependencies:
 SuperLU                     i686     6.0.1-1.fc40            local       201 k
 SuperLU-devel               i686     6.0.1-1.fc40            local        27 k
 annobin-docs                noarch   12.33-1.fc40            local        91 k
 annobin-plugin-gcc          i686     12.33-1.fc40            local       959 k
 armadillo                   i686     10.8.2-5.fc39           local        41 k
 arpack                      i686     3.9.1-1.fc40            local       123 k
 arpack-devel                i686     3.9.1-1.fc40            local        13 k
 autoconf                    noarch   2.71-7.fc40             local       720 k
 automake                    noarch   1.16.5-14.fc40          local       676 k
 boost                       i686     1.83.0-0.fc40           copr_base    14 k
 boost-atomic                i686     1.83.0-0.fc40           copr_base    20 k
 boost-chrono                i686     1.83.0-0.fc40           copr_base    28 k
 boost-container             i686     1.83.0-0.fc40           copr_base    41 k
 boost-context               i686     1.83.0-0.fc40           copr_base    17 k
 boost-contract              i686     1.83.0-0.fc40           copr_base    49 k
 boost-coroutine             i686     1.83.0-0.fc40           copr_base    21 k
 boost-date-time             i686     1.83.0-0.fc40           copr_base    16 k
 boost-fiber                 i686     1.83.0-0.fc40           copr_base    45 k
 boost-filesystem            i686     1.83.0-0.fc40           copr_base    73 k
 boost-graph                 i686     1.83.0-0.fc40           copr_base   159 k
 boost-iostreams             i686     1.83.0-0.fc40           copr_base    45 k
 boost-json                  i686     1.83.0-0.fc40           copr_base   160 k
 boost-locale                i686     1.83.0-0.fc40           copr_base   235 k
 boost-log                   i686     1.83.0-0.fc40           copr_base   532 k
 boost-math                  i686     1.83.0-0.fc40           copr_base   216 k
 boost-nowide                i686     1.83.0-0.fc40           copr_base    22 k
 boost-numpy3                i686     1.83.0-0.fc40           copr_base    31 k
 boost-program-options       i686     1.83.0-0.fc40           copr_base   118 k
 boost-python3               i686     1.83.0-0.fc40           copr_base   104 k
 boost-random                i686     1.83.0-0.fc40           copr_base    25 k
 boost-regex                 i686     1.83.0-0.fc40           copr_base   116 k
 boost-serialization         i686     1.83.0-0.fc40           copr_base   145 k
 boost-stacktrace            i686     1.83.0-0.fc40           copr_base    32 k
 boost-system                i686     1.83.0-0.fc40           copr_base    16 k
 boost-test                  i686     1.83.0-0.fc40           copr_base   257 k
 boost-thread                i686     1.83.0-0.fc40           copr_base    66 k
 boost-timer                 i686     1.83.0-0.fc40           copr_base    23 k
 boost-type_erasure          i686     1.83.0-0.fc40           copr_base    35 k
 boost-wave                  i686     1.83.0-0.fc40           copr_base   231 k
 cmake-filesystem            i686     3.27.7-1.fc40           local        19 k
 cpp                         i686     13.2.1-6.fc40           local        11 M
 emacs-filesystem            noarch   1:29.1-14.fc40          local       7.4 k
 expat                       i686     2.5.0-3.fc39            local       114 k
 flexiblas                   i686     3.3.1-5.fc39            local        33 k
 flexiblas-netlib            i686     3.3.1-5.fc39            local       3.1 M
 flexiblas-openblas-openmp   i686     3.3.1-5.fc39            local        17 k
 gc                          i686     8.2.2-4.fc39            local       113 k
 gcc                         i686     13.2.1-6.fc40           local        34 M
 gcc-gfortran                i686     13.2.1-6.fc40           local        12 M
 gcc-plugin-annobin          i686     13.2.1-6.fc40           local        50 k
 glibc-devel                 i686     2.38.9000-26.fc40       local        96 k
 glibc-headers-x86           noarch   2.38.9000-26.fc40       local       510 k
 groff-base                  i686     1.23.0-3.fc40           local       1.1 M
 gsl                         i686     2.7.1-5.fc39            local       1.2 M
 guile22                     i686     2.2.7-9.fc39            local       6.5 M
 hdf5                        i686     1.12.1-15.fc40          local       2.1 M
 hdf5-devel                  i686     1.12.1-15.fc40          local       1.3 M
 htslib                      i686     1.15.1-3.fc39           local       527 k
 kernel-headers              i686     6.7.0-0.rc5.41.fc40     local       1.4 M
 libaec                      i686     1.0.6-5.fc39            local        44 k
 libaec-devel                i686     1.0.6-5.fc39            local        12 k
 libasan                     i686     13.2.1-6.fc40           local       509 k
 libatomic                   i686     13.2.1-6.fc40           local        36 k
 libb2                       i686     0.98.1-9.fc39           local        28 k
 libgfortran                 i686     13.2.1-6.fc40           local       843 k
 libicu                      i686     73.2-2.fc39             local        11 M
 libicu-devel                i686     73.2-2.fc39             local       849 k
 libmpc                      i686     1.3.1-3.fc39            local        77 k
 libquadmath                 i686     13.2.1-6.fc40           local       245 k
 libquadmath-devel           i686     13.2.1-6.fc40           local        39 k
 libstdc++-devel             i686     13.2.1-6.fc40           local       2.5 M
 libtool-ltdl                i686     2.4.7-8.fc40            local        38 k
 libubsan                    i686     13.2.1-6.fc40           local       237 k
 libxcrypt-devel             i686     4.4.36-2.fc39           local        30 k
 m4                          i686     1.4.19-7.fc40           local       300 k
 metis                       i686     5.1.0.3-2.fc39          local       581 k
 mpdecimal                   i686     2.5.1-7.fc39            local        91 k
 ncurses                     i686     6.4-8.20231001.fc40     local       414 k
 openblas                    i686     0.3.25-1.fc40           local        38 k
 openblas-openmp             i686     0.3.25-1.fc40           local       3.9 M
 perl-AutoLoader             noarch   5.74-503.fc40           local        21 k
 perl-B                      i686     1.88-503.fc40           local       181 k
 perl-Carp                   noarch   1.54-500.fc39           local        29 k
 perl-Class-Struct           noarch   0.68-503.fc40           local        22 k
 perl-Data-Dumper            i686     2.188-501.fc39          local        58 k
 perl-Digest                 noarch   1.20-500.fc39           local        25 k
 perl-Digest-MD5             i686     2.58-501.fc40           local        36 k
 perl-DynaLoader             i686     1.54-503.fc40           local        26 k
 perl-Encode                 i686     4:3.20-501.fc40         local       1.2 M
 perl-Errno                  i686     1.37-503.fc40           local        15 k
 perl-Exporter               noarch   5.77-500.fc39           local        31 k
 perl-Fcntl                  i686     1.15-503.fc40           local        21 k
 perl-Fedora-VSP             noarch   0.001-32.fc39           local        23 k
 perl-File-Basename          noarch   2.86-503.fc40           local        17 k
 perl-File-Compare           noarch   1.100.700-503.fc40      local        13 k
 perl-File-Copy              noarch   2.41-503.fc40           local        20 k
 perl-File-Find              noarch   1.43-503.fc40           local        26 k
 perl-File-Path              noarch   2.18-501.fc40           local        35 k
 perl-File-Temp              noarch   1:0.231.100-501.fc40    local        59 k
 perl-File-stat              noarch   1.13-503.fc40           local        17 k
 perl-FileHandle             noarch   2.05-503.fc40           local        16 k
 perl-Getopt-Long            noarch   1:2.57-1.fc40           local        63 k
 perl-Getopt-Std             noarch   1.13-503.fc40           local        16 k
 perl-HTTP-Tiny              noarch   0.088-3.fc39            local        56 k
 perl-IO                     i686     1.52-503.fc40           local        79 k
 perl-IO-Socket-IP           noarch   0.42-1.fc39             local        42 k
 perl-IO-Socket-SSL          noarch   2.084-1.fc40            local       221 k
 perl-IPC-Open3              noarch   1.22-503.fc40           local        22 k
 perl-MIME-Base64            i686     3.16-501.fc40           local        30 k
 perl-Mozilla-CA             noarch   20230821-1.fc40         local        13 k
 perl-Net-SSLeay             i686     1.92-10.fc39            local       350 k
 perl-POSIX                  i686     2.13-503.fc40           local       101 k
 perl-PathTools              i686     3.89-500.fc39           local        83 k
 perl-Pod-Escapes            noarch   1:1.07-501.fc40         local        19 k
 perl-Pod-Perldoc            noarch   3.28.01-501.fc39        local        80 k
 perl-Pod-Simple             noarch   1:3.45-4.fc39           local       208 k
 perl-Pod-Usage              noarch   4:2.03-500.fc39         local        39 k
 perl-Scalar-List-Utils      i686     5:1.63-500.fc39         local        75 k
 perl-SelectSaver            noarch   1.02-503.fc40           local        12 k
 perl-Socket                 i686     4:2.037-3.fc39          local        56 k
 perl-Storable               i686     1:3.32-500.fc39         local       101 k
 perl-Symbol                 noarch   1.09-503.fc40           local        14 k
 perl-Term-ANSIColor         noarch   5.01-502.fc40           local        47 k
 perl-Term-Cap               noarch   1.18-500.fc39           local        22 k
 perl-Text-ParseWords        noarch   3.31-500.fc39           local        16 k
 perl-Text-Tabs+Wrap         noarch   2023.0511-3.fc39        local        22 k
 perl-Thread-Queue           noarch   3.14-501.fc40           local        21 k
 perl-Time-Local             noarch   2:1.350-3.fc39          local        34 k
 perl-URI                    noarch   5.21-1.fc40             local       113 k
 perl-base                   noarch   2.27-503.fc40           local        16 k
 perl-constant               noarch   1.33-501.fc39           local        22 k
 perl-if                     noarch   0.61.000-503.fc40       local        14 k
 perl-interpreter            i686     4:5.38.2-503.fc40       local        72 k
 perl-libnet                 noarch   3.15-501.fc39           local       122 k
 perl-libs                   i686     4:5.38.2-503.fc40       local       2.3 M
 perl-locale                 noarch   1.10-503.fc40           local        14 k
 perl-macros                 noarch   4:5.38.2-503.fc40       local        13 k
 perl-mro                    i686     1.28-503.fc40           local        30 k
 perl-overload               noarch   1.37-503.fc40           local        46 k
 perl-overloading            noarch   0.02-503.fc40           local        13 k
 perl-parent                 noarch   1:0.241-500.fc39        local        14 k
 perl-podlators              noarch   1:5.01-500.fc39         local       120 k
 perl-threads                i686     1:2.36-500.fc39         local        60 k
 perl-threads-shared         i686     1.68-500.fc39           local        46 k
 perl-vars                   noarch   1.05-503.fc40           local        13 k
 python-pip-wheel            noarch   23.2.1-1.fc39           local       1.5 M
 python3                     i686     3.12.1-1.fc40           local        26 k
 python3-libs                i686     3.12.1-1.fc40           local       9.0 M
 python3-numpy               i686     1:1.26.0-2.fc40         local       6.8 M
 tzdata                      noarch   2023c-4.fc40            local       433 k

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

Total size: 155 M
Total download size: 23 M
Installed size: 633 M
Downloading Packages:
[SKIPPED] boost-1.83.0-0.fc40.i686.rpm: Already downloaded                     
[SKIPPED] boost-atomic-1.83.0-0.fc40.i686.rpm: Already downloaded              
[SKIPPED] boost-chrono-1.83.0-0.fc40.i686.rpm: Already downloaded              
[SKIPPED] boost-container-1.83.0-0.fc40.i686.rpm: Already downloaded           
[SKIPPED] boost-context-1.83.0-0.fc40.i686.rpm: Already downloaded             
[SKIPPED] boost-contract-1.83.0-0.fc40.i686.rpm: Already downloaded            
[SKIPPED] boost-coroutine-1.83.0-0.fc40.i686.rpm: Already downloaded           
[SKIPPED] boost-date-time-1.83.0-0.fc40.i686.rpm: Already downloaded           
[SKIPPED] boost-devel-1.83.0-0.fc40.i686.rpm: Already downloaded               
[SKIPPED] boost-fiber-1.83.0-0.fc40.i686.rpm: Already downloaded               
[SKIPPED] boost-filesystem-1.83.0-0.fc40.i686.rpm: Already downloaded          
[SKIPPED] boost-graph-1.83.0-0.fc40.i686.rpm: Already downloaded               
[SKIPPED] boost-iostreams-1.83.0-0.fc40.i686.rpm: Already downloaded           
[SKIPPED] boost-json-1.83.0-0.fc40.i686.rpm: Already downloaded                
[SKIPPED] boost-locale-1.83.0-0.fc40.i686.rpm: Already downloaded              
[SKIPPED] boost-log-1.83.0-0.fc40.i686.rpm: Already downloaded                 
[SKIPPED] boost-math-1.83.0-0.fc40.i686.rpm: Already downloaded                
[SKIPPED] boost-nowide-1.83.0-0.fc40.i686.rpm: Already downloaded              
[SKIPPED] boost-numpy3-1.83.0-0.fc40.i686.rpm: Already downloaded              
[SKIPPED] boost-program-options-1.83.0-0.fc40.i686.rpm: Already downloaded     
[SKIPPED] boost-python3-1.83.0-0.fc40.i686.rpm: Already downloaded             
[SKIPPED] boost-random-1.83.0-0.fc40.i686.rpm: Already downloaded              
[SKIPPED] boost-regex-1.83.0-0.fc40.i686.rpm: Already downloaded               
[SKIPPED] boost-serialization-1.83.0-0.fc40.i686.rpm: Already downloaded       
[SKIPPED] boost-stacktrace-1.83.0-0.fc40.i686.rpm: Already downloaded          
[SKIPPED] boost-system-1.83.0-0.fc40.i686.rpm: Already downloaded              
[SKIPPED] boost-test-1.83.0-0.fc40.i686.rpm: Already downloaded                
[SKIPPED] boost-thread-1.83.0-0.fc40.i686.rpm: Already downloaded              
[SKIPPED] boost-timer-1.83.0-0.fc40.i686.rpm: Already downloaded               
[SKIPPED] boost-type_erasure-1.83.0-0.fc40.i686.rpm: Already downloaded        
[SKIPPED] boost-wave-1.83.0-0.fc40.i686.rpm: Already downloaded                
[SKIPPED] annobin-docs-12.33-1.fc40.noarch.rpm: Already downloaded             
[SKIPPED] annobin-plugin-gcc-12.33-1.fc40.i686.rpm: Already downloaded         
[SKIPPED] cpp-13.2.1-6.fc40.i686.rpm: Already downloaded                       
[SKIPPED] expat-2.5.0-3.fc39.i686.rpm: Already downloaded                      
[SKIPPED] flexiblas-3.3.1-5.fc39.i686.rpm: Already downloaded                  
[SKIPPED] flexiblas-netlib-3.3.1-5.fc39.i686.rpm: Already downloaded           
[SKIPPED] flexiblas-openblas-openmp-3.3.1-5.fc39.i686.rpm: Already downloaded  
[SKIPPED] gc-8.2.2-4.fc39.i686.rpm: Already downloaded                         
[SKIPPED] gcc-13.2.1-6.fc40.i686.rpm: Already downloaded                       
[SKIPPED] gcc-c++-13.2.1-6.fc40.i686.rpm: Already downloaded                   
[SKIPPED] gcc-plugin-annobin-13.2.1-6.fc40.i686.rpm: Already downloaded        
[SKIPPED] glibc-devel-2.38.9000-26.fc40.i686.rpm: Already downloaded           
[SKIPPED] glibc-headers-x86-2.38.9000-26.fc40.noarch.rpm: Already downloaded   
[SKIPPED] groff-base-1.23.0-3.fc40.i686.rpm: Already downloaded                
[SKIPPED] guile22-2.2.7-9.fc39.i686.rpm: Already downloaded                    
[SKIPPED] kernel-headers-6.7.0-0.rc5.41.fc40.i686.rpm: Already downloaded      
[SKIPPED] libasan-13.2.1-6.fc40.i686.rpm: Already downloaded                   
[SKIPPED] libatomic-13.2.1-6.fc40.i686.rpm: Already downloaded                 
[SKIPPED] libb2-0.98.1-9.fc39.i686.rpm: Already downloaded                     
[SKIPPED] libgfortran-13.2.1-6.fc40.i686.rpm: Already downloaded               
[SKIPPED] libicu-73.2-2.fc39.i686.rpm: Already downloaded                      
[SKIPPED] libicu-devel-73.2-2.fc39.i686.rpm: Already downloaded                
[SKIPPED] libmpc-1.3.1-3.fc39.i686.rpm: Already downloaded                     
[SKIPPED] libquadmath-13.2.1-6.fc40.i686.rpm: Already downloaded               
[SKIPPED] libquadmath-devel-13.2.1-6.fc40.i686.rpm: Already downloaded         
[SKIPPED] libstdc++-devel-13.2.1-6.fc40.i686.rpm: Already downloaded           
[SKIPPED] libtool-ltdl-2.4.7-8.fc40.i686.rpm: Already downloaded               
[SKIPPED] libubsan-13.2.1-6.fc40.i686.rpm: Already downloaded                  
[SKIPPED] libxcrypt-devel-4.4.36-2.fc39.i686.rpm: Already downloaded           
[SKIPPED] make-4.4.1-2.fc39.i686.rpm: Already downloaded                       
[SKIPPED] mpdecimal-2.5.1-7.fc39.i686.rpm: Already downloaded                  
[SKIPPED] ncurses-6.4-8.20231001.fc40.i686.rpm: Already downloaded             
[SKIPPED] openblas-0.3.25-1.fc40.i686.rpm: Already downloaded                  
[SKIPPED] openblas-openmp-0.3.25-1.fc40.i686.rpm: Already downloaded           
[SKIPPED] perl-AutoLoader-5.74-503.fc40.noarch.rpm: Already downloaded         
[SKIPPED] perl-B-1.88-503.fc40.i686.rpm: Already downloaded                    
[SKIPPED] perl-Carp-1.54-500.fc39.noarch.rpm: Already downloaded               
[SKIPPED] perl-Class-Struct-0.68-503.fc40.noarch.rpm: Already downloaded       
[SKIPPED] perl-Data-Dumper-2.188-501.fc39.i686.rpm: Already downloaded         
[SKIPPED] perl-Digest-1.20-500.fc39.noarch.rpm: Already downloaded             
[SKIPPED] perl-Digest-MD5-2.58-501.fc40.i686.rpm: Already downloaded           
[SKIPPED] perl-DynaLoader-1.54-503.fc40.i686.rpm: Already downloaded           
[SKIPPED] perl-Encode-3.20-501.fc40.i686.rpm: Already downloaded               
[SKIPPED] perl-Errno-1.37-503.fc40.i686.rpm: Already downloaded                
[SKIPPED] perl-Exporter-5.77-500.fc39.noarch.rpm: Already downloaded           
[SKIPPED] perl-Fcntl-1.15-503.fc40.i686.rpm: Already downloaded                
[SKIPPED] perl-File-Basename-2.86-503.fc40.noarch.rpm: Already downloaded      
[SKIPPED] perl-File-Path-2.18-501.fc40.noarch.rpm: Already downloaded          
[SKIPPED] perl-File-Temp-0.231.100-501.fc40.noarch.rpm: Already downloaded     
[SKIPPED] perl-File-stat-1.13-503.fc40.noarch.rpm: Already downloaded          
[SKIPPED] perl-FileHandle-2.05-503.fc40.noarch.rpm: Already downloaded         
[SKIPPED] perl-Getopt-Long-2.57-1.fc40.noarch.rpm: Already downloaded          
[SKIPPED] perl-Getopt-Std-1.13-503.fc40.noarch.rpm: Already downloaded         
[SKIPPED] perl-HTTP-Tiny-0.088-3.fc39.noarch.rpm: Already downloaded           
[SKIPPED] perl-IO-1.52-503.fc40.i686.rpm: Already downloaded                   
[SKIPPED] perl-IO-Socket-IP-0.42-1.fc39.noarch.rpm: Already downloaded         
[SKIPPED] perl-IO-Socket-SSL-2.084-1.fc40.noarch.rpm: Already downloaded       
[SKIPPED] perl-IPC-Open3-1.22-503.fc40.noarch.rpm: Already downloaded          
[SKIPPED] perl-MIME-Base64-3.16-501.fc40.i686.rpm: Already downloaded          
[SKIPPED] perl-Mozilla-CA-20230821-1.fc40.noarch.rpm: Already downloaded       
[SKIPPED] perl-Net-SSLeay-1.92-10.fc39.i686.rpm: Already downloaded            
[SKIPPED] perl-POSIX-2.13-503.fc40.i686.rpm: Already downloaded                
[SKIPPED] perl-PathTools-3.89-500.fc39.i686.rpm: Already downloaded            
[SKIPPED] perl-Pod-Escapes-1.07-501.fc40.noarch.rpm: Already downloaded        
[SKIPPED] perl-Pod-Perldoc-3.28.01-501.fc39.noarch.rpm: Already downloaded     
[SKIPPED] perl-Pod-Simple-3.45-4.fc39.noarch.rpm: Already downloaded           
[SKIPPED] perl-Pod-Usage-2.03-500.fc39.noarch.rpm: Already downloaded          
[SKIPPED] perl-Scalar-List-Utils-1.63-500.fc39.i686.rpm: Already downloaded    
[SKIPPED] perl-SelectSaver-1.02-503.fc40.noarch.rpm: Already downloaded        
[SKIPPED] perl-Socket-2.037-3.fc39.i686.rpm: Already downloaded                
[SKIPPED] perl-Storable-3.32-500.fc39.i686.rpm: Already downloaded             
[SKIPPED] perl-Symbol-1.09-503.fc40.noarch.rpm: Already downloaded             
[SKIPPED] perl-Term-ANSIColor-5.01-502.fc40.noarch.rpm: Already downloaded     
[SKIPPED] perl-Term-Cap-1.18-500.fc39.noarch.rpm: Already downloaded           
[SKIPPED] perl-Text-ParseWords-3.31-500.fc39.noarch.rpm: Already downloaded    
[SKIPPED] perl-Text-Tabs+Wrap-2023.0511-3.fc39.noarch.rpm: Already downloaded  
[SKIPPED] perl-Time-Local-1.350-3.fc39.noarch.rpm: Already downloaded          
[SKIPPED] perl-URI-5.21-1.fc40.noarch.rpm: Already downloaded                  
[SKIPPED] perl-base-2.27-503.fc40.noarch.rpm: Already downloaded               
[SKIPPED] perl-constant-1.33-501.fc39.noarch.rpm: Already downloaded           
[SKIPPED] perl-if-0.61.000-503.fc40.noarch.rpm: Already downloaded             
[SKIPPED] perl-interpreter-5.38.2-503.fc40.i686.rpm: Already downloaded        
[SKIPPED] perl-libnet-3.15-501.fc39.noarch.rpm: Already downloaded             
[SKIPPED] perl-libs-5.38.2-503.fc40.i686.rpm: Already downloaded               
[SKIPPED] perl-locale-1.10-503.fc40.noarch.rpm: Already downloaded             
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Total                                            18 MB/s |  23 MB     00:01     
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Installed:
  SuperLU-6.0.1-1.fc40.i686                                                     
  SuperLU-devel-6.0.1-1.fc40.i686                                               
  annobin-docs-12.33-1.fc40.noarch                                              
  annobin-plugin-gcc-12.33-1.fc40.i686                                          
  armadillo-10.8.2-5.fc39.i686                                                  
  armadillo-devel-10.8.2-5.fc39.i686                                            
  arpack-3.9.1-1.fc40.i686                                                      
  arpack-devel-3.9.1-1.fc40.i686                                                
  autoconf-2.71-7.fc40.noarch                                                   
  automake-1.16.5-14.fc40.noarch                                                
  boost-1.83.0-0.fc40.i686                                                      
  boost-atomic-1.83.0-0.fc40.i686                                               
  boost-chrono-1.83.0-0.fc40.i686                                               
  boost-container-1.83.0-0.fc40.i686                                            
  boost-context-1.83.0-0.fc40.i686                                              
  boost-contract-1.83.0-0.fc40.i686                                             
  boost-coroutine-1.83.0-0.fc40.i686                                            
  boost-date-time-1.83.0-0.fc40.i686                                            
  boost-devel-1.83.0-0.fc40.i686                                                
  boost-fiber-1.83.0-0.fc40.i686                                                
  boost-filesystem-1.83.0-0.fc40.i686                                           
  boost-graph-1.83.0-0.fc40.i686                                                
  boost-iostreams-1.83.0-0.fc40.i686                                            
  boost-json-1.83.0-0.fc40.i686                                                 
  boost-locale-1.83.0-0.fc40.i686                                               
  boost-log-1.83.0-0.fc40.i686                                                  
  boost-math-1.83.0-0.fc40.i686                                                 
  boost-nowide-1.83.0-0.fc40.i686                                               
  boost-numpy3-1.83.0-0.fc40.i686                                               
  boost-program-options-1.83.0-0.fc40.i686                                      
  boost-python3-1.83.0-0.fc40.i686                                              
  boost-random-1.83.0-0.fc40.i686                                               
  boost-regex-1.83.0-0.fc40.i686                                                
  boost-serialization-1.83.0-0.fc40.i686                                        
  boost-stacktrace-1.83.0-0.fc40.i686                                           
  boost-system-1.83.0-0.fc40.i686                                               
  boost-test-1.83.0-0.fc40.i686                                                 
  boost-thread-1.83.0-0.fc40.i686                                               
  boost-timer-1.83.0-0.fc40.i686                                                
  boost-type_erasure-1.83.0-0.fc40.i686                                         
  boost-wave-1.83.0-0.fc40.i686                                                 
  cmake-filesystem-3.27.7-1.fc40.i686                                           
  cpp-13.2.1-6.fc40.i686                                                        
  emacs-filesystem-1:29.1-14.fc40.noarch                                        
  expat-2.5.0-3.fc39.i686                                                       
  flexiblas-3.3.1-5.fc39.i686                                                   
  flexiblas-devel-3.3.1-5.fc39.i686                                             
  flexiblas-netlib-3.3.1-5.fc39.i686                                            
  flexiblas-openblas-openmp-3.3.1-5.fc39.i686                                   
  gc-8.2.2-4.fc39.i686                                                          
  gcc-13.2.1-6.fc40.i686                                                        
  gcc-c++-13.2.1-6.fc40.i686                                                    
  gcc-gfortran-13.2.1-6.fc40.i686                                               
  gcc-plugin-annobin-13.2.1-6.fc40.i686                                         
  glibc-devel-2.38.9000-26.fc40.i686                                            
  glibc-headers-x86-2.38.9000-26.fc40.noarch                                    
  groff-base-1.23.0-3.fc40.i686                                                 
  gsl-2.7.1-5.fc39.i686                                                         
  gsl-devel-2.7.1-5.fc39.i686                                                   
  guile22-2.2.7-9.fc39.i686                                                     
  hdf5-1.12.1-15.fc40.i686                                                      
  hdf5-devel-1.12.1-15.fc40.i686                                                
  htslib-1.15.1-3.fc39.i686                                                     
  htslib-devel-1.15.1-3.fc39.i686                                               
  kernel-headers-6.7.0-0.rc5.41.fc40.i686                                       
  libaec-1.0.6-5.fc39.i686                                                      
  libaec-devel-1.0.6-5.fc39.i686                                                
  libasan-13.2.1-6.fc40.i686                                                    
  libatomic-13.2.1-6.fc40.i686                                                  
  libb2-0.98.1-9.fc39.i686                                                      
  libgfortran-13.2.1-6.fc40.i686                                                
  libicu-73.2-2.fc39.i686                                                       
  libicu-devel-73.2-2.fc39.i686                                                 
  libmpc-1.3.1-3.fc39.i686                                                      
  libquadmath-13.2.1-6.fc40.i686                                                
  libquadmath-devel-13.2.1-6.fc40.i686                                          
  libstdc++-devel-13.2.1-6.fc40.i686                                            
  libtool-ltdl-2.4.7-8.fc40.i686                                                
  libubsan-13.2.1-6.fc40.i686                                                   
  libxcrypt-devel-4.4.36-2.fc39.i686                                            
  m4-1.4.19-7.fc40.i686                                                         
  make-1:4.4.1-2.fc39.i686                                                      
  metis-5.1.0.3-2.fc39.i686                                                     
  mpdecimal-2.5.1-7.fc39.i686                                                   
  ncurses-6.4-8.20231001.fc40.i686                                              
  openblas-0.3.25-1.fc40.i686                                                   
  openblas-openmp-0.3.25-1.fc40.i686                                            
  perl-AutoLoader-5.74-503.fc40.noarch                                          
  perl-B-1.88-503.fc40.i686                                                     
  perl-Carp-1.54-500.fc39.noarch                                                
  perl-Class-Struct-0.68-503.fc40.noarch                                        
  perl-Data-Dumper-2.188-501.fc39.i686                                          
  perl-Digest-1.20-500.fc39.noarch                                              
  perl-Digest-MD5-2.58-501.fc40.i686                                            
  perl-DynaLoader-1.54-503.fc40.i686                                            
  perl-Encode-4:3.20-501.fc40.i686                                              
  perl-Errno-1.37-503.fc40.i686                                                 
  perl-Exporter-5.77-500.fc39.noarch                                            
  perl-Fcntl-1.15-503.fc40.i686                                                 
  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.i686                                                    
  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.i686                                           
  perl-Mozilla-CA-20230821-1.fc40.noarch                                        
  perl-Net-SSLeay-1.92-10.fc39.i686                                             
  perl-POSIX-2.13-503.fc40.i686                                                 
  perl-PathTools-3.89-500.fc39.i686                                             
  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.i686                                   
  perl-SelectSaver-1.02-503.fc40.noarch                                         
  perl-Socket-4:2.037-3.fc39.i686                                               
  perl-Storable-1:3.32-500.fc39.i686                                            
  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.i686                                       
  perl-libnet-3.15-501.fc39.noarch                                              
  perl-libs-4:5.38.2-503.fc40.i686                                              
  perl-locale-1.10-503.fc40.noarch                                              
  perl-macros-4:5.38.2-503.fc40.noarch                                          
  perl-mro-1.28-503.fc40.i686                                                   
  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.i686                                             
  perl-threads-shared-1.68-500.fc39.i686                                        
  perl-vars-1.05-503.fc40.noarch                                                
  python-pip-wheel-23.2.1-1.fc39.noarch                                         
  python3-3.12.1-1.fc40.i686                                                    
  python3-libs-3.12.1-1.fc40.i686                                               
  python3-numpy-1:1.26.0-2.fc40.i686                                            
  tzdata-2023c-4.fc40.noarch                                                    
  zlib-devel-1.2.13-5.fc40.i686                                                 

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: i686
Building for target i686
setting SOURCE_DATE_EPOCH=1689811200
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.am2wxE
+ 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.7TvNnT
+ 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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection '
+ 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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection '
+ 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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -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/lib:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd mmseq-1.0.11
+ cd src
+ make -j2 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection    -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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 offsetGTF.cpp -o ../bin/offsetGTF
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 ‘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 ‘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 ‘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 ‘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;
      |                ^~~~~~~~~~
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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  237 |       if(i < tokens.size()-1) {
      |          ~~^~~~~~~~~~~~~~~~~
offsetGTF.cpp:108:7: warning: unused variable ‘gff_pos’ [-Wunused-variable]
  108 |   int gff_pos= -1;
      |       ^~~~~~~
hitsio.cpp: In member function ‘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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 ‘unsigned int’} [-Wsign-compare]
   90 |         for(int i=2; i < tokens.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~
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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -O3 uh.o sokal.o mmcollapse.cpp -o ../bin/mmcollapse -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema0()’:
hitsio.cpp:163:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  236 |         for(int i = 0; i < currentReadTranscripts.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileReader::readHeaderSchema1(std::vector<std::__cxx11::basic_string<char> >*, std::map<std::__cxx11::basic_string<char>, double>*, std::map<std::__cxx11::basic_string<char>, int>*, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >*, std::vector<std::vector<std::__cxx11::basic_string<char> > >*)’:
hitsio.cpp:356:16: warning: unused variable ‘nextStrLen’ [-Wunused-variable]
  356 |         size_t nextStrLen;
      |                ^~~~~~~~~~
hitsio.cpp: In member function ‘bool HitsfileReader::readReadMapRecordTranscriptID(std::string&)’:
hitsio.cpp:447:1: warning: control reaches end of non-void function [-Wreturn-type]
  447 | }
      | ^
mmcollapse.cpp: In function ‘void get_unidentifiable_transcripts(std::string, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> >&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> >&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> >&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::map<std::__cxx11::basic_string<char>, bool>&)’:
mmcollapse.cpp:158:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘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 ‘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 ‘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 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 ‘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 ‘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 ‘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 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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 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 ‘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 ‘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 ‘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 ‘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 ‘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 unsigned int’} [-Wsign-compare]
 1092 |     for(int v = 0; v < M.n_cols; v++) {
      |                    ~~^~~~~~~~~~
mmcollapse.cpp:840:9: warning: unused variable ‘isident’ [-Wunused-variable]
  840 |     int isident=0;
      |         ^~~~~~~
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -O2 bms.cpp bms.hpp -c bms.cpp
bms.cpp: In member function ‘arma::Col<int> BMS::m2v(arma::Mat<double>)’:
bms.cpp:36:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ‘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 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 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 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 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 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 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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 unsigned int’} [-Wsign-compare]
  638 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
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 ‘unsigned int’} [-Wsign-compare]
  130 |   for(int i=0;i < v.size(); i++) {
      |               ~~^~~~~~~~~~
bms.cpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const 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 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 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 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 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 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 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 unsigned int’} [-Wsign-compare]
  699 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
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 ‘unsigned int’} [-Wsign-compare]
  244 |       for(int i=0; i < tokens.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~
bms.cpp:704:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 unsigned int’} [-Wsign-compare]
 1106 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
mmseq.cpp:423:20: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix<bool>::size_type’ {aka ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  940 |   for(int i=0; i < identical_transcripts.size() * trace_length; i++) mu_trace_identical[i]=0;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 unsigned int’} [-Wsign-compare]
 1188 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
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 ‘unsigned int’} [-Wsign-compare]
  961 |   for(int i=0; i < gene2transcripts.size() * trace_length; i++) mu_trace_gene[i]=0;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bms.cpp:1192:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘unsigned int’} [-Wsign-compare]
 1192 |         if(C(i,model)+1 > _n.size()) {
      |            ~~~~~~~~~~~~~^~~~~~~~~~~
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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 1168 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
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 unsigned int’} [-Wsign-compare]
 1348 |   for(int i=0; i < M.n_cols; i++) {
      |                ~~^~~~~~~~~~
mmseq.cpp:1179:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
 1227 |   for(int i=0; i < gene2transcripts.size(); i++) meanmu_gene[i]/= trace_length;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~
bms.cpp:1354:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const 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 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 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 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 unsigned int’} [-Wsign-compare]
 1378 |   for(int i=0; i < P[1].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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;
      |        ^~~~~~~~~
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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -O3 fasta.o hitsio.o bam2hits.cpp -o ../bin/bam2hits -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
bam2hits.cpp: In function ‘void outputMergeHeaders(std::vector<FastaRecord>&, char, const char*, bool, HitsfileWriter&)’:
bam2hits.cpp:109:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  997 |       for(int fl=1; fl <= (it->seq()).size(); fl++) {
      |                     ~~~^~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:1091:56: warning: comparing the result of pointer addition ‘(bam_aux_get(((const bam1_t*)line), ((const char*)"NM")) + ((sizetype)ait.__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >::operator->()->Alignment::NM()))’ and NULL [-Waddress]
 1091 |             ait->NM(ait->NM() + bam_aux_get(line,"NM") == NULL ? 0 : bam_aux2i(bam_aux_get(line,"NM")));
      |                                                        ^
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 fasta.o extract_transcripts.cpp -o ../bin/extract_transcripts
extract_transcripts.cpp: In function ‘int main(int, char**)’:
extract_transcripts.cpp:122:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  203 |       while(faline < stitch.size()) {
      |             ~~~~~~~^~~~~~~~~~~~~~~
extract_transcripts.cpp:108:7: warning: unused variable ‘line’ [-Wunused-variable]
  108 |   int line=0;
      |       ^~~~
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 ‘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 ‘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 ‘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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 ‘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 ‘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 ‘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 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 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 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 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 ‘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 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 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 ‘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 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 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 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 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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 ‘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 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 ‘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 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 ‘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 ‘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 ‘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 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 ‘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 ‘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 ‘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 ‘unsigned int’} [-Wsign-compare]
  951 |       for(int feature=0; feature < features.size(); feature++) {
      |                          ~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/bin/ld: /tmp/ccadtXN7.ltrans0.ltrans.o: in function `main':
/builddir/build/BUILD/mmseq-1.0.11/src/bam2hits.cpp:653:(.text.startup+0x40e1): 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.qUvuOM
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386
++ dirname /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386
+ 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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection '
+ 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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection '
+ 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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -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/lib:
+ 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.i386
+ mkdir -p /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/bin
+ install -p -m 0755 bin/bam2hits /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/bin
+ install -p -m 0755 bin/extract_transcripts /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/bin
+ install -p -m 0755 bin/hitstools /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/bin
+ install -p -m 0755 bin/mmcollapse /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/bin
+ install -p -m 0755 bin/mmdiff /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/bin
+ install -p -m 0755 bin/mmseq /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/bin
+ install -p -m 0755 bin/offsetGTF /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/bin
+ install -p -m 0755 bin/t2g_hits /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/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.i386/usr/bin
+ install -p -m 0755 bin/filterGTF.rb bin/haploref.rb bin/testregexp.rb /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/bin
+ install -p -m 0755 bin/ensembl_gtf_to_gff.pl /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/bin
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.0.11-16.fc40 --unique-debug-suffix -1.0.11-16.fc40.i386 --unique-debug-src-base mmseq-1.0.11-16.fc40.i386 --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.i386
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 -j2
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.20os1y
+ 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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection '
+ 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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection '
+ 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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/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  -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -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/lib:
+ 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.i686
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.hF0Nv5
+ umask 022
+ cd /builddir/build/BUILD
+ cd mmseq-1.0.11
+ DOCDIR=/builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/share/doc/mmseq
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/share/doc/mmseq
+ cp -pr /builddir/build/BUILD/mmseq-1.0.11/README.md /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/share/doc/mmseq
+ cp -pr /builddir/build/BUILD/mmseq-1.0.11/COPYING /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/share/doc/mmseq
+ cp -pr /builddir/build/BUILD/mmseq-1.0.11/doc /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386/usr/share/doc/mmseq
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: mmseq = 1.0.11-16.fc40 mmseq(x86-32) = 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 libboost_iostreams.so.1.83.0 libboost_regex.so.1.83.0 libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.32) libc.so.6(GLIBC_2.33) libc.so.6(GLIBC_2.34) libc.so.6(GLIBC_2.38) libc.so.6(GLIBC_2.4) libflexiblas.so.3 libgcc_s.so.1 libgcc_s.so.1(GCC_3.0) libgcc_s.so.1(GCC_3.3.1) libgomp.so.1 libgomp.so.1(GOMP_1.0) libgomp.so.1(GOMP_4.0) libgomp.so.1(OMP_1.0) libgsl.so.27 libgslcblas.so.0 libhts.so.3 libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libm.so.6(GLIBC_2.29) libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(CXXABI_1.3.8) libstdc++.so.6(CXXABI_1.3.9) libstdc++.so.6(GLIBCXX_3.4) libstdc++.so.6(GLIBCXX_3.4.11) libstdc++.so.6(GLIBCXX_3.4.15) libstdc++.so.6(GLIBCXX_3.4.20) libstdc++.so.6(GLIBCXX_3.4.21) libstdc++.so.6(GLIBCXX_3.4.26) libstdc++.so.6(GLIBCXX_3.4.29) libstdc++.so.6(GLIBCXX_3.4.30) libstdc++.so.6(GLIBCXX_3.4.32) libstdc++.so.6(GLIBCXX_3.4.9) perl(strict) rtld(GNU_HASH)
Processing files: mmseq-debugsource-1.0.11-16.fc40.i686
Provides: mmseq-debugsource = 1.0.11-16.fc40 mmseq-debugsource(x86-32) = 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.i686
Provides: debuginfo(build-id) = 090124453e660ed68c20971663a2d457b09c61c1 debuginfo(build-id) = 27f9b1c66f76d080bc93b404811c0c91eb10c8e1 debuginfo(build-id) = 7d7a0552a28c0a2e2b53eb53a8ad4cfb41eda1d9 debuginfo(build-id) = 8f6b0304123c742fbbcc4672ed680b0380fac2cd debuginfo(build-id) = 95af20e6c780f7fb4f95df2e885f62a125c7b05a debuginfo(build-id) = ba194f44c19a20bb2995244bff3db3bd72031ef4 debuginfo(build-id) = de1f990e4b32a2dfd4f9e193813f4e36fad06528 debuginfo(build-id) = f83288b5b39c0817ded175a0b657daa0b6c57d44 mmseq-debuginfo = 1.0.11-16.fc40 mmseq-debuginfo(x86-32) = 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(x86-32) = 1.0.11-16.fc40
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386
Wrote: /builddir/build/RPMS/mmseq-1.0.11-16.fc40.i686.rpm
Wrote: /builddir/build/RPMS/mmseq-debugsource-1.0.11-16.fc40.i686.rpm
Wrote: /builddir/build/RPMS/mmseq-debuginfo-1.0.11-16.fc40.i686.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.1dFvAI
+ umask 022
+ cd /builddir/build/BUILD
+ cd mmseq-1.0.11
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/mmseq-1.0.11-16.fc40.i386
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.RasReC
+ 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-i686-1702420631.229914/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-i686-1702420631.229914/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-i686-1702420631.229914/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/mmseq-1.0.11-16.fc40.src.rpm) Config(child) 1 minutes 38 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "mmseq-debugsource",
            "epoch": null,
            "version": "1.0.11",
            "release": "16.fc40",
            "arch": "i686"
        },
        {
            "name": "mmseq",
            "epoch": null,
            "version": "1.0.11",
            "release": "16.fc40",
            "arch": "src"
        },
        {
            "name": "mmseq",
            "epoch": null,
            "version": "1.0.11",
            "release": "16.fc40",
            "arch": "i686"
        },
        {
            "name": "mmseq-debuginfo",
            "epoch": null,
            "version": "1.0.11",
            "release": "16.fc40",
            "arch": "i686"
        }
    ]
}
RPMResults finished