Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c189' (ED25519) to the list of known hosts.
Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5925876 --chroot fedora-rawhide-x86_64 --detached
Version: 0.64
PID: 7159
Logging PID: 7160
Task:
{'appstream': False,
 'background': False,
 'build_id': 5925876,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '5167d7337230a82f2f5a8cb9e72fc960a158e4b6',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/fi-muni/bioinformatics/mafft',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'mafft',
 'package_version': '7.520-1.20230516222539466786.mafft',
 'project_dirname': 'bioinformatics',
 'project_name': 'bioinformatics',
 'project_owner': 'fi-muni',
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/fi-muni/bioinformatics/fedora-rawhide-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository'}],
 'sandbox': 'fi-muni/bioinformatics--packit',
 'source_json': {},
 'source_type': None,
 'submitter': 'packit',
 'tags': [],
 'task_id': '5925876-fedora-rawhide-x86_64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/fi-muni/bioinformatics/mafft /var/lib/copr-rpmbuild/workspace/workdir-12e58v47/mafft --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/fi-muni/bioinformatics/mafft', '/var/lib/copr-rpmbuild/workspace/workdir-12e58v47/mafft', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-12e58v47/mafft'...

Running: git checkout 5167d7337230a82f2f5a8cb9e72fc960a158e4b6

cmd: ['git', 'checkout', '5167d7337230a82f2f5a8cb9e72fc960a158e4b6']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-12e58v47/mafft
rc: 0
stdout: 
stderr: Note: switching to '5167d7337230a82f2f5a8cb9e72fc960a158e4b6'.

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 5167d73 automatic import of mafft

Running: copr-distgit-client sources

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-12e58v47/mafft
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 mafft-7.520.tar.gz
INFO: Calling: curl -H Pragma: -o mafft-7.520.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/fi-muni/bioinformatics/mafft/mafft-7.520.tar.gz/md5/8d53ef6ecf6822d00c9d356f59f5aabe/mafft-7.520.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  722k  100  722k    0     0  6908k      0 --:--:-- --:--:-- --:--:-- 6949k
INFO: Reading stdout from command: md5sum mafft-7.520.tar.gz

/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=18000): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-12e58v47/mafft/mafft.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-12e58v47/mafft --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1684275986.169171 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)...
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-12e58v47/mafft/mafft.spec)  Config(fedora-rawhide-x86_64)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1684275986.169171/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: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start(bootstrap): dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Updating Subscription Management repositories.
Unable to read consumer identity

This system is not registered with an entitlement server. You can use subscription-manager to register.

Copr repository                                 715  B/s | 257  B     00:00    
fedora                                           14 MB/s |  71 MB     00:04    
Dependencies resolved.
================================================================================
 Package                       Arch   Version                      Repo    Size
================================================================================
Installing:
 dnf                           noarch 4.15.0-1.fc39                fedora 476 k
 dnf-plugins-core              noarch 4.4.1-1.fc39                 fedora  38 k
Installing dependencies:
 alternatives                  x86_64 1.24-1.fc39                  fedora  39 k
 audit-libs                    x86_64 3.1.1-1.fc39                 fedora 117 k
 basesystem                    noarch 11-15.fc38                   fedora 7.0 k
 bash                          x86_64 5.2.15-3.fc38                fedora 1.8 M
 bzip2-libs                    x86_64 1.0.8-13.fc38                fedora  41 k
 ca-certificates               noarch 2023.2.60-2.fc38             fedora 845 k
 coreutils                     x86_64 9.3-1.fc39                   fedora 1.1 M
 coreutils-common              x86_64 9.3-1.fc39                   fedora 2.1 M
 crypto-policies               noarch 20230420-1.git3d08ae7.fc39   fedora  94 k
 curl                          x86_64 8.0.1-3.fc39                 fedora 350 k
 cyrus-sasl-lib                x86_64 2.1.28-10.fc39               fedora 792 k
 dbus-libs                     x86_64 1:1.14.6-1.fc38              fedora 156 k
 dnf-data                      noarch 4.15.0-1.fc39                fedora  39 k
 elfutils-default-yama-scope   noarch 0.189-2.fc39                 fedora  15 k
 elfutils-libelf               x86_64 0.189-2.fc39                 fedora 196 k
 elfutils-libs                 x86_64 0.189-2.fc39                 fedora 260 k
 expat                         x86_64 2.5.0-2.fc38                 fedora 110 k
 fedora-gpg-keys               noarch 39-0.1                       fedora 126 k
 fedora-release                noarch 39-0.11                      fedora  12 k
 fedora-release-common         noarch 39-0.11                      fedora  22 k
 fedora-release-identity-basic noarch 39-0.11                      fedora  13 k
 fedora-repos                  noarch 39-0.1                       fedora 9.4 k
 fedora-repos-rawhide          noarch 39-0.1                       fedora 9.0 k
 file-libs                     x86_64 5.44-3.fc39                  fedora 730 k
 filesystem                    x86_64 3.18-4.fc39                  fedora 1.1 M
 findutils                     x86_64 1:4.9.0-4.fc39               fedora 491 k
 gawk                          x86_64 5.1.1-5.fc38                 fedora 1.0 M
 gdbm-libs                     x86_64 1:1.23-3.fc38                fedora  56 k
 glib2                         x86_64 2.76.2-1.fc39                fedora 2.8 M
 glibc                         x86_64 2.37.9000-9.fc39             fedora 2.1 M
 glibc-common                  x86_64 2.37.9000-9.fc39             fedora 330 k
 glibc-minimal-langpack        x86_64 2.37.9000-9.fc39             fedora  52 k
 gmp                           x86_64 1:6.2.1-4.fc38               fedora 313 k
 gnupg2                        x86_64 2.4.1-1.fc39                 fedora 2.6 M
 gnutls                        x86_64 3.8.0-3.fc39                 fedora 1.1 M
 gpgme                         x86_64 1.17.1-5.fc39                fedora 206 k
 grep                          x86_64 3.9-1.fc39                   fedora 295 k
 ima-evm-utils                 x86_64 1.4-7.fc38                   fedora  62 k
 json-c                        x86_64 0.16-4.fc38                  fedora  41 k
 keyutils-libs                 x86_64 1.6.1-6.fc38                 fedora  31 k
 krb5-libs                     x86_64 1.20.1-9.fc39                fedora 727 k
 libacl                        x86_64 2.3.1-7.fc39                 fedora  23 k
 libarchive                    x86_64 3.6.1-5.fc39                 fedora 400 k
 libassuan                     x86_64 2.5.5-6.fc38                 fedora  67 k
 libattr                       x86_64 2.5.1-7.fc39                 fedora  18 k
 libb2                         x86_64 0.98.1-8.fc38                fedora  25 k
 libblkid                      x86_64 2.39-0.5.fc39                fedora 116 k
 libbrotli                     x86_64 1.0.9-11.fc38                fedora 317 k
 libcap                        x86_64 2.48-6.fc38                  fedora  67 k
 libcap-ng                     x86_64 0.8.3-5.fc38                 fedora  32 k
 libcom_err                    x86_64 1.46.5-4.fc38                fedora  26 k
 libcomps                      x86_64 0.1.19-1.fc39                fedora  77 k
 libcurl                       x86_64 8.0.1-3.fc39                 fedora 313 k
 libdnf                        x86_64 0.70.1-1.fc39                fedora 667 k
 libeconf                      x86_64 0.4.0-5.fc38                 fedora  27 k
 libevent                      x86_64 2.1.12-8.fc38                fedora 257 k
 libffi                        x86_64 3.4.4-2.fc38                 fedora  38 k
 libfsverity                   x86_64 1.4-9.fc38                   fedora  19 k
 libgcc                        x86_64 13.1.1-2.fc39                fedora 106 k
 libgcrypt                     x86_64 1.10.2-1.fc39                fedora 514 k
 libgomp                       x86_64 13.1.1-2.fc39                fedora 316 k
 libgpg-error                  x86_64 1.47-1.fc39                  fedora 230 k
 libidn2                       x86_64 2.3.4-2.fc38                 fedora 160 k
 libksba                       x86_64 1.6.3-2.fc38                 fedora 159 k
 libmodulemd                   x86_64 2.15.0-2.fc39                fedora 231 k
 libmount                      x86_64 2.39-0.5.fc39                fedora 153 k
 libnghttp2                    x86_64 1.53.0-1.fc39                fedora  75 k
 libnsl2                       x86_64 2.0.0-5.fc38                 fedora  30 k
 libpsl                        x86_64 0.21.2-2.fc38                fedora  65 k
 librepo                       x86_64 1.15.1-2.fc38                fedora  96 k
 libreport-filesystem          noarch 2.17.10-1.fc39               fedora  14 k
 libselinux                    x86_64 3.5-1.fc39                   fedora  87 k
 libsemanage                   x86_64 3.5-2.fc39                   fedora 120 k
 libsepol                      x86_64 3.5-1.fc39                   fedora 324 k
 libsigsegv                    x86_64 2.14-4.fc38                  fedora  27 k
 libsmartcols                  x86_64 2.39-0.5.fc39                fedora  67 k
 libsolv                       x86_64 0.7.24-2.fc39                fedora 425 k
 libssh                        x86_64 0.10.5-1.fc39                fedora 211 k
 libssh-config                 noarch 0.10.5-1.fc39                fedora 9.0 k
 libstdc++                     x86_64 13.1.1-2.fc39                fedora 860 k
 libtasn1                      x86_64 4.19.0-2.fc38                fedora  74 k
 libtirpc                      x86_64 1.3.3-1.rc1.fc39             fedora  93 k
 libunistring                  x86_64 1.1-3.fc38                   fedora 545 k
 libunistring1.0               x86_64 1.0-1.fc38                   fedora 539 k
 libuuid                       x86_64 2.39-0.5.fc39                fedora  28 k
 libverto                      x86_64 0.3.2-5.fc38                 fedora  21 k
 libxcrypt                     x86_64 4.4.33-7.fc39                fedora 120 k
 libxml2                       x86_64 2.10.4-1.fc39                fedora 700 k
 libyaml                       x86_64 0.2.5-9.fc38                 fedora  59 k
 libzstd                       x86_64 1.5.5-1.fc39                 fedora 308 k
 lua-libs                      x86_64 5.4.4-9.fc39                 fedora 133 k
 lz4-libs                      x86_64 1.9.4-3.fc39                 fedora  67 k
 mpdecimal                     x86_64 2.5.1-6.fc38                 fedora  89 k
 mpfr                          x86_64 4.1.1-3.fc38                 fedora 600 k
 ncurses-base                  noarch 6.4-3.20230114.fc38          fedora  87 k
 ncurses-libs                  x86_64 6.4-3.20230114.fc38          fedora 333 k
 nettle                        x86_64 3.8-3.fc38                   fedora 412 k
 npth                          x86_64 1.6-12.fc38                  fedora  24 k
 openldap                      x86_64 2.6.4-2.fc39                 fedora 255 k
 openssl-libs                  x86_64 1:3.0.8-2.fc39               fedora 2.1 M
 p11-kit                       x86_64 0.24.1-6.fc38                fedora 359 k
 p11-kit-trust                 x86_64 0.24.1-6.fc38                fedora 136 k
 pcre2                         x86_64 10.42-1.fc38.1               fedora 234 k
 pcre2-syntax                  noarch 10.42-1.fc38.1               fedora 144 k
 popt                          x86_64 1.19-2.fc38                  fedora  67 k
 publicsuffix-list-dafsa       noarch 20230318-1.fc39              fedora  60 k
 python-pip-wheel              noarch 23.0.1-2.fc39                fedora 1.4 M
 python-setuptools-wheel       noarch 67.7.2-1.fc39                fedora 661 k
 python3                       x86_64 3.11.3-1.fc39                fedora  28 k
 python3-dateutil              noarch 1:2.8.2-6.fc39               fedora 360 k
 python3-dbus                  x86_64 1.3.2-2.fc38                 fedora 157 k
 python3-distro                noarch 1.8.0-3.fc39                 fedora  49 k
 python3-dnf                   noarch 4.15.0-1.fc39                fedora 603 k
 python3-dnf-plugins-core      noarch 4.4.1-1.fc39                 fedora 299 k
 python3-gpg                   x86_64 1.17.1-5.fc39                fedora 295 k
 python3-hawkey                x86_64 0.70.1-1.fc39                fedora 107 k
 python3-libcomps              x86_64 0.1.19-1.fc39                fedora  47 k
 python3-libdnf                x86_64 0.70.1-1.fc39                fedora 826 k
 python3-libs                  x86_64 3.11.3-1.fc39                fedora 9.6 M
 python3-rpm                   x86_64 4.18.1-3.fc39                fedora  72 k
 python3-six                   noarch 1.16.0-9.fc38                fedora  42 k
 python3-systemd               x86_64 235-2.fc38                   fedora 108 k
 readline                      x86_64 8.2-3.fc38                   fedora 212 k
 rpm                           x86_64 4.18.1-3.fc39                fedora 571 k
 rpm-build-libs                x86_64 4.18.1-3.fc39                fedora  94 k
 rpm-libs                      x86_64 4.18.1-3.fc39                fedora 312 k
 rpm-sequoia                   x86_64 1.4.0-2.fc39                 fedora 849 k
 rpm-sign-libs                 x86_64 4.18.1-3.fc39                fedora  26 k
 sed                           x86_64 4.8-12.fc38                  fedora 306 k
 setup                         noarch 2.14.3-3.fc39                fedora 152 k
 shadow-utils                  x86_64 2:4.13-6.fc39                fedora 1.3 M
 sqlite-libs                   x86_64 3.41.2-1.fc39                fedora 669 k
 systemd-libs                  x86_64 253.4-1.fc39                 fedora 652 k
 tpm2-tss                      x86_64 4.0.1-3.fc38                 fedora 675 k
 tzdata                        noarch 2023c-1.fc39                 fedora 718 k
 xz-libs                       x86_64 5.4.3-1.fc39                 fedora 108 k
 zchunk-libs                   x86_64 1.3.1-1.fc39                 fedora  52 k
 zlib                          x86_64 1.2.13-3.fc38                fedora  95 k

Transaction Summary
================================================================================
Install  140 Packages

Total download size: 58 M
Installed size: 204 M
Downloading Packages:
(1/140): basesystem-11-15.fc38.noarch.rpm        29 kB/s | 7.0 kB     00:00    
(2/140): alternatives-1.24-1.fc39.x86_64.rpm    117 kB/s |  39 kB     00:00    
(3/140): audit-libs-3.1.1-1.fc39.x86_64.rpm     346 kB/s | 117 kB     00:00    
(4/140): bzip2-libs-1.0.8-13.fc38.x86_64.rpm    373 kB/s |  41 kB     00:00    
(5/140): bash-5.2.15-3.fc38.x86_64.rpm          6.2 MB/s | 1.8 MB     00:00    
(6/140): coreutils-9.3-1.fc39.x86_64.rpm        9.9 MB/s | 1.1 MB     00:00    
(7/140): ca-certificates-2023.2.60-2.fc38.noarc 3.6 MB/s | 845 kB     00:00    
(8/140): coreutils-common-9.3-1.fc39.x86_64.rpm  31 MB/s | 2.1 MB     00:00    
(9/140): crypto-policies-20230420-1.git3d08ae7. 2.2 MB/s |  94 kB     00:00    
(10/140): curl-8.0.1-3.fc39.x86_64.rpm          7.7 MB/s | 350 kB     00:00    
(11/140): cyrus-sasl-lib-2.1.28-10.fc39.x86_64.  16 MB/s | 792 kB     00:00    
(12/140): dbus-libs-1.14.6-1.fc38.x86_64.rpm    3.1 MB/s | 156 kB     00:00    
(13/140): dnf-4.15.0-1.fc39.noarch.rpm           10 MB/s | 476 kB     00:00    
(14/140): dnf-data-4.15.0-1.fc39.noarch.rpm     1.0 MB/s |  39 kB     00:00    
(15/140): dnf-plugins-core-4.4.1-1.fc39.noarch. 1.0 MB/s |  38 kB     00:00    
(16/140): elfutils-default-yama-scope-0.189-2.f 401 kB/s |  15 kB     00:00    
(17/140): elfutils-libelf-0.189-2.fc39.x86_64.r 4.9 MB/s | 196 kB     00:00    
(18/140): elfutils-libs-0.189-2.fc39.x86_64.rpm 6.3 MB/s | 260 kB     00:00    
(19/140): expat-2.5.0-2.fc38.x86_64.rpm         2.1 MB/s | 110 kB     00:00    
(20/140): fedora-gpg-keys-39-0.1.noarch.rpm     3.2 MB/s | 126 kB     00:00    
(21/140): fedora-release-39-0.11.noarch.rpm     328 kB/s |  12 kB     00:00    
(22/140): fedora-release-common-39-0.11.noarch. 453 kB/s |  22 kB     00:00    
(23/140): fedora-release-identity-basic-39-0.11 317 kB/s |  13 kB     00:00    
(24/140): fedora-repos-39-0.1.noarch.rpm        231 kB/s | 9.4 kB     00:00    
(25/140): fedora-repos-rawhide-39-0.1.noarch.rp 213 kB/s | 9.0 kB     00:00    
(26/140): file-libs-5.44-3.fc39.x86_64.rpm       16 MB/s | 730 kB     00:00    
(27/140): filesystem-3.18-4.fc39.x86_64.rpm      11 MB/s | 1.1 MB     00:00    
(28/140): findutils-4.9.0-4.fc39.x86_64.rpm     6.4 MB/s | 491 kB     00:00    
(29/140): gawk-5.1.1-5.fc38.x86_64.rpm           18 MB/s | 1.0 MB     00:00    
(30/140): gdbm-libs-1.23-3.fc38.x86_64.rpm      1.4 MB/s |  56 kB     00:00    
(31/140): glib2-2.76.2-1.fc39.x86_64.rpm         25 MB/s | 2.8 MB     00:00    
(32/140): glibc-2.37.9000-9.fc39.x86_64.rpm      14 MB/s | 2.1 MB     00:00    
(33/140): glibc-common-2.37.9000-9.fc39.x86_64. 2.8 MB/s | 330 kB     00:00    
(34/140): glibc-minimal-langpack-2.37.9000-9.fc 1.3 MB/s |  52 kB     00:00    
(35/140): gmp-6.2.1-4.fc38.x86_64.rpm           7.3 MB/s | 313 kB     00:00    
(36/140): gnupg2-2.4.1-1.fc39.x86_64.rpm         24 MB/s | 2.6 MB     00:00    
(37/140): gnutls-3.8.0-3.fc39.x86_64.rpm        8.1 MB/s | 1.1 MB     00:00    
(38/140): gpgme-1.17.1-5.fc39.x86_64.rpm        2.1 MB/s | 206 kB     00:00    
(39/140): grep-3.9-1.fc39.x86_64.rpm            6.5 MB/s | 295 kB     00:00    
(40/140): ima-evm-utils-1.4-7.fc38.x86_64.rpm   1.6 MB/s |  62 kB     00:00    
(41/140): json-c-0.16-4.fc38.x86_64.rpm         720 kB/s |  41 kB     00:00    
(42/140): keyutils-libs-1.6.1-6.fc38.x86_64.rpm 701 kB/s |  31 kB     00:00    
(43/140): krb5-libs-1.20.1-9.fc39.x86_64.rpm    6.9 MB/s | 727 kB     00:00    
(44/140): libacl-2.3.1-7.fc39.x86_64.rpm        278 kB/s |  23 kB     00:00    
(45/140): libarchive-3.6.1-5.fc39.x86_64.rpm    4.7 MB/s | 400 kB     00:00    
(46/140): libassuan-2.5.5-6.fc38.x86_64.rpm     1.7 MB/s |  67 kB     00:00    
(47/140): libattr-2.5.1-7.fc39.x86_64.rpm       454 kB/s |  18 kB     00:00    
(48/140): libb2-0.98.1-8.fc38.x86_64.rpm        638 kB/s |  25 kB     00:00    
(49/140): libblkid-2.39-0.5.fc39.x86_64.rpm     1.4 MB/s | 116 kB     00:00    
(50/140): libbrotli-1.0.9-11.fc38.x86_64.rpm    3.7 MB/s | 317 kB     00:00    
(51/140): libcap-2.48-6.fc38.x86_64.rpm         799 kB/s |  67 kB     00:00    
(52/140): libcap-ng-0.8.3-5.fc38.x86_64.rpm     393 kB/s |  32 kB     00:00    
(53/140): libcom_err-1.46.5-4.fc38.x86_64.rpm   324 kB/s |  26 kB     00:00    
(54/140): libcomps-0.1.19-1.fc39.x86_64.rpm     972 kB/s |  77 kB     00:00    
(55/140): libcurl-8.0.1-3.fc39.x86_64.rpm       6.7 MB/s | 313 kB     00:00    
(56/140): libdnf-0.70.1-1.fc39.x86_64.rpm       7.8 MB/s | 667 kB     00:00    
(57/140): libeconf-0.4.0-5.fc38.x86_64.rpm      320 kB/s |  27 kB     00:00    
(58/140): libevent-2.1.12-8.fc38.x86_64.rpm     5.9 MB/s | 257 kB     00:00    
(59/140): libffi-3.4.4-2.fc38.x86_64.rpm        1.0 MB/s |  38 kB     00:00    
(60/140): libfsverity-1.4-9.fc38.x86_64.rpm     507 kB/s |  19 kB     00:00    
(61/140): libgcc-13.1.1-2.fc39.x86_64.rpm       2.7 MB/s | 106 kB     00:00    
(62/140): libgcrypt-1.10.2-1.fc39.x86_64.rpm     11 MB/s | 514 kB     00:00    
(63/140): libgomp-13.1.1-2.fc39.x86_64.rpm      4.2 MB/s | 316 kB     00:00    
(64/140): libgpg-error-1.47-1.fc39.x86_64.rpm   3.1 MB/s | 230 kB     00:00    
(65/140): libidn2-2.3.4-2.fc38.x86_64.rpm       4.0 MB/s | 160 kB     00:00    
(66/140): libksba-1.6.3-2.fc38.x86_64.rpm       4.0 MB/s | 159 kB     00:00    
(67/140): libmodulemd-2.15.0-2.fc39.x86_64.rpm  5.8 MB/s | 231 kB     00:00    
(68/140): libmount-2.39-0.5.fc39.x86_64.rpm     3.4 MB/s | 153 kB     00:00    
(69/140): libnghttp2-1.53.0-1.fc39.x86_64.rpm   1.7 MB/s |  75 kB     00:00    
(70/140): libnsl2-2.0.0-5.fc38.x86_64.rpm       720 kB/s |  30 kB     00:00    
(71/140): libpsl-0.21.2-2.fc38.x86_64.rpm       1.7 MB/s |  65 kB     00:00    
(72/140): librepo-1.15.1-2.fc38.x86_64.rpm      2.2 MB/s |  96 kB     00:00    
(73/140): libreport-filesystem-2.17.10-1.fc39.n 329 kB/s |  14 kB     00:00    
(74/140): libselinux-3.5-1.fc39.x86_64.rpm      2.2 MB/s |  87 kB     00:00    
(75/140): libsemanage-3.5-2.fc39.x86_64.rpm     3.0 MB/s | 120 kB     00:00    
(76/140): libsepol-3.5-1.fc39.x86_64.rpm        7.6 MB/s | 324 kB     00:00    
(77/140): libsigsegv-2.14-4.fc38.x86_64.rpm     668 kB/s |  27 kB     00:00    
(78/140): libsmartcols-2.39-0.5.fc39.x86_64.rpm 1.7 MB/s |  67 kB     00:00    
(79/140): libsolv-0.7.24-2.fc39.x86_64.rpm       10 MB/s | 425 kB     00:00    
(80/140): libssh-0.10.5-1.fc39.x86_64.rpm       4.9 MB/s | 211 kB     00:00    
(81/140): libssh-config-0.10.5-1.fc39.noarch.rp 206 kB/s | 9.0 kB     00:00    
(82/140): libstdc++-13.1.1-2.fc39.x86_64.rpm     11 MB/s | 860 kB     00:00    
(83/140): libtasn1-4.19.0-2.fc38.x86_64.rpm     982 kB/s |  74 kB     00:00    
(84/140): libtirpc-1.3.3-1.rc1.fc39.x86_64.rpm  2.3 MB/s |  93 kB     00:00    
(85/140): libunistring-1.1-3.fc38.x86_64.rpm     11 MB/s | 545 kB     00:00    
(86/140): libunistring1.0-1.0-1.fc38.x86_64.rpm 6.5 MB/s | 539 kB     00:00    
(87/140): libuuid-2.39-0.5.fc39.x86_64.rpm      348 kB/s |  28 kB     00:00    
(88/140): libverto-0.3.2-5.fc38.x86_64.rpm      552 kB/s |  21 kB     00:00    
(89/140): libxcrypt-4.4.33-7.fc39.x86_64.rpm    3.1 MB/s | 120 kB     00:00    
(90/140): libxml2-2.10.4-1.fc39.x86_64.rpm      9.1 MB/s | 700 kB     00:00    
(91/140): libyaml-0.2.5-9.fc38.x86_64.rpm       817 kB/s |  59 kB     00:00    
(92/140): libzstd-1.5.5-1.fc39.x86_64.rpm       7.5 MB/s | 308 kB     00:00    
(93/140): lua-libs-5.4.4-9.fc39.x86_64.rpm      3.4 MB/s | 133 kB     00:00    
(94/140): lz4-libs-1.9.4-3.fc39.x86_64.rpm      1.7 MB/s |  67 kB     00:00    
(95/140): mpdecimal-2.5.1-6.fc38.x86_64.rpm     2.3 MB/s |  89 kB     00:00    
(96/140): mpfr-4.1.1-3.fc38.x86_64.rpm           14 MB/s | 600 kB     00:00    
(97/140): ncurses-base-6.4-3.20230114.fc38.noar 1.9 MB/s |  87 kB     00:00    
(98/140): ncurses-libs-6.4-3.20230114.fc38.x86_ 4.4 MB/s | 333 kB     00:00    
(99/140): nettle-3.8-3.fc38.x86_64.rpm          8.8 MB/s | 412 kB     00:00    
(100/140): npth-1.6-12.fc38.x86_64.rpm          533 kB/s |  24 kB     00:00    
(101/140): openldap-2.6.4-2.fc39.x86_64.rpm     5.8 MB/s | 255 kB     00:00    
(102/140): openssl-libs-3.0.8-2.fc39.x86_64.rpm  15 MB/s | 2.1 MB     00:00    
(103/140): p11-kit-0.24.1-6.fc38.x86_64.rpm     2.3 MB/s | 359 kB     00:00    
(104/140): p11-kit-trust-0.24.1-6.fc38.x86_64.r 1.1 MB/s | 136 kB     00:00    
(105/140): pcre2-10.42-1.fc38.1.x86_64.rpm      5.7 MB/s | 234 kB     00:00    
(106/140): pcre2-syntax-10.42-1.fc38.1.noarch.r 3.6 MB/s | 144 kB     00:00    
(107/140): popt-1.19-2.fc38.x86_64.rpm          1.7 MB/s |  67 kB     00:00    
(108/140): publicsuffix-list-dafsa-20230318-1.f 1.6 MB/s |  60 kB     00:00    
(109/140): python-pip-wheel-23.0.1-2.fc39.noarc  17 MB/s | 1.4 MB     00:00    
(110/140): python-setuptools-wheel-67.7.2-1.fc3 5.5 MB/s | 661 kB     00:00    
(111/140): python3-3.11.3-1.fc39.x86_64.rpm     297 kB/s |  28 kB     00:00    
(112/140): python3-dateutil-2.8.2-6.fc39.noarch 5.3 MB/s | 360 kB     00:00    
(113/140): python3-dbus-1.3.2-2.fc38.x86_64.rpm 3.9 MB/s | 157 kB     00:00    
(114/140): python3-distro-1.8.0-3.fc39.noarch.r 1.2 MB/s |  49 kB     00:00    
(115/140): python3-dnf-4.15.0-1.fc39.noarch.rpm  13 MB/s | 603 kB     00:00    
(116/140): python3-dnf-plugins-core-4.4.1-1.fc3 4.3 MB/s | 299 kB     00:00    
(117/140): python3-gpg-1.17.1-5.fc39.x86_64.rpm 3.9 MB/s | 295 kB     00:00    
(118/140): python3-hawkey-0.70.1-1.fc39.x86_64. 2.5 MB/s | 107 kB     00:00    
(119/140): python3-libcomps-0.1.19-1.fc39.x86_6 1.2 MB/s |  47 kB     00:00    
(120/140): python3-libdnf-0.70.1-1.fc39.x86_64.  10 MB/s | 826 kB     00:00    
(121/140): python3-six-1.16.0-9.fc38.noarch.rpm 256 kB/s |  42 kB     00:00    
(122/140): python3-rpm-4.18.1-3.fc39.x86_64.rpm 249 kB/s |  72 kB     00:00    
(123/140): python3-systemd-235-2.fc38.x86_64.rp 302 kB/s | 108 kB     00:00    
(124/140): python3-libs-3.11.3-1.fc39.x86_64.rp  13 MB/s | 9.6 MB     00:00    
(125/140): readline-8.2-3.fc38.x86_64.rpm       536 kB/s | 212 kB     00:00    
(126/140): rpm-4.18.1-3.fc39.x86_64.rpm         3.6 MB/s | 571 kB     00:00    
(127/140): rpm-build-libs-4.18.1-3.fc39.x86_64. 2.3 MB/s |  94 kB     00:00    
(128/140): rpm-libs-4.18.1-3.fc39.x86_64.rpm    5.1 MB/s | 312 kB     00:00    
(129/140): rpm-sequoia-1.4.0-2.fc39.x86_64.rpm   10 MB/s | 849 kB     00:00    
(130/140): rpm-sign-libs-4.18.1-3.fc39.x86_64.r 339 kB/s |  26 kB     00:00    
(131/140): sed-4.8-12.fc38.x86_64.rpm           4.5 MB/s | 306 kB     00:00    
(132/140): setup-2.14.3-3.fc39.noarch.rpm       3.4 MB/s | 152 kB     00:00    
(133/140): shadow-utils-4.13-6.fc39.x86_64.rpm  9.6 MB/s | 1.3 MB     00:00    
(134/140): sqlite-libs-3.41.2-1.fc39.x86_64.rpm 3.4 MB/s | 669 kB     00:00    
(135/140): systemd-libs-253.4-1.fc39.x86_64.rpm 3.1 MB/s | 652 kB     00:00    
(136/140): tpm2-tss-4.0.1-3.fc38.x86_64.rpm     3.6 MB/s | 675 kB     00:00    
(137/140): tzdata-2023c-1.fc39.noarch.rpm       3.8 MB/s | 718 kB     00:00    
(138/140): xz-libs-5.4.3-1.fc39.x86_64.rpm      766 kB/s | 108 kB     00:00    
(139/140): zchunk-libs-1.3.1-1.fc39.x86_64.rpm  686 kB/s |  52 kB     00:00    
(140/140): zlib-1.2.13-3.fc38.x86_64.rpm        2.2 MB/s |  95 kB     00:00    
--------------------------------------------------------------------------------
Total                                            14 MB/s |  58 MB     00:04     
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0x18B8E74C:
 Userid     : "Fedora (39) <fedora-39-primary@fedoraproject.org>"
 Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary
Key imported successfully
fedora                                          1.6 MB/s | 1.6 kB     00:00    
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary (0x18B8E74C) is already installed
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0xEB10B464:
 Userid     : "Fedora (38) <fedora-38-primary@fedoraproject.org>"
 Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.18-4.fc39.x86_64                          1/1 
  Preparing        :                                                        1/1 
  Installing       : libgcc-13.1.1-2.fc39.x86_64                          1/140 
  Running scriptlet: libgcc-13.1.1-2.fc39.x86_64                          1/140 
  Installing       : tzdata-2023c-1.fc39.noarch                           2/140 
  Installing       : crypto-policies-20230420-1.git3d08ae7.fc39.noarc     3/140 
  Running scriptlet: crypto-policies-20230420-1.git3d08ae7.fc39.noarc     3/140 
  Installing       : fedora-release-identity-basic-39-0.11.noarch         4/140 
  Installing       : python-setuptools-wheel-67.7.2-1.fc39.noarch         5/140 
  Installing       : publicsuffix-list-dafsa-20230318-1.fc39.noarch       6/140 
  Installing       : pcre2-syntax-10.42-1.fc38.1.noarch                   7/140 
  Installing       : ncurses-base-6.4-3.20230114.fc38.noarch              8/140 
  Installing       : libssh-config-0.10.5-1.fc39.noarch                   9/140 
  Installing       : libreport-filesystem-2.17.10-1.fc39.noarch          10/140 
  Installing       : dnf-data-4.15.0-1.fc39.noarch                       11/140 
warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew

  Installing       : fedora-gpg-keys-39-0.1.noarch                       12/140 
  Installing       : fedora-release-39-0.11.noarch                       13/140 
  Installing       : fedora-release-common-39-0.11.noarch                14/140 
  Installing       : fedora-repos-rawhide-39-0.1.noarch                  15/140 
  Installing       : fedora-repos-39-0.1.noarch                          16/140 
  Installing       : setup-2.14.3-3.fc39.noarch                          17/140 
  Running scriptlet: setup-2.14.3-3.fc39.noarch                          17/140 
  Installing       : filesystem-3.18-4.fc39.x86_64                       18/140 
  Installing       : basesystem-11-15.fc38.noarch                        19/140 
  Installing       : glibc-minimal-langpack-2.37.9000-9.fc39.x86_64      20/140 
  Installing       : glibc-common-2.37.9000-9.fc39.x86_64                21/140 
  Running scriptlet: glibc-2.37.9000-9.fc39.x86_64                       22/140 
  Installing       : glibc-2.37.9000-9.fc39.x86_64                       22/140 
  Running scriptlet: glibc-2.37.9000-9.fc39.x86_64                       22/140 
  Installing       : ncurses-libs-6.4-3.20230114.fc38.x86_64             23/140 
  Installing       : bash-5.2.15-3.fc38.x86_64                           24/140 
  Running scriptlet: bash-5.2.15-3.fc38.x86_64                           24/140 
  Installing       : zlib-1.2.13-3.fc38.x86_64                           25/140 
  Installing       : bzip2-libs-1.0.8-13.fc38.x86_64                     26/140 
  Installing       : libzstd-1.5.5-1.fc39.x86_64                         27/140 
  Installing       : xz-libs-5.4.3-1.fc39.x86_64                         28/140 
  Installing       : sqlite-libs-3.41.2-1.fc39.x86_64                    29/140 
  Installing       : libcap-2.48-6.fc38.x86_64                           30/140 
  Installing       : gmp-1:6.2.1-4.fc38.x86_64                           31/140 
  Installing       : libgpg-error-1.47-1.fc39.x86_64                     32/140 
  Installing       : popt-1.19-2.fc38.x86_64                             33/140 
  Installing       : libxml2-2.10.4-1.fc39.x86_64                        34/140 
  Installing       : libuuid-2.39-0.5.fc39.x86_64                        35/140 
  Installing       : lua-libs-5.4.4-9.fc39.x86_64                        36/140 
  Installing       : elfutils-libelf-0.189-2.fc39.x86_64                 37/140 
  Installing       : readline-8.2-3.fc38.x86_64                          38/140 
  Installing       : libattr-2.5.1-7.fc39.x86_64                         39/140 
  Installing       : libacl-2.3.1-7.fc39.x86_64                          40/140 
  Installing       : libffi-3.4.4-2.fc38.x86_64                          41/140 
  Installing       : p11-kit-0.24.1-6.fc38.x86_64                        42/140 
  Installing       : libstdc++-13.1.1-2.fc39.x86_64                      43/140 
  Installing       : libxcrypt-4.4.33-7.fc39.x86_64                      44/140 
  Installing       : pcre2-10.42-1.fc38.1.x86_64                         45/140 
  Installing       : libassuan-2.5.5-6.fc38.x86_64                       46/140 
  Installing       : file-libs-5.44-3.fc39.x86_64                        47/140 
  Installing       : expat-2.5.0-2.fc38.x86_64                           48/140 
  Installing       : gdbm-libs-1:1.23-3.fc38.x86_64                      49/140 
  Installing       : json-c-0.16-4.fc38.x86_64                           50/140 
  Installing       : keyutils-libs-1.6.1-6.fc38.x86_64                   51/140 
  Installing       : libcom_err-1.46.5-4.fc38.x86_64                     52/140 
  Installing       : libgomp-13.1.1-2.fc39.x86_64                        53/140 
  Installing       : libsepol-3.5-1.fc39.x86_64                          54/140 
  Installing       : libselinux-3.5-1.fc39.x86_64                        55/140 
  Installing       : sed-4.8-12.fc38.x86_64                              56/140 
  Installing       : libsmartcols-2.39-0.5.fc39.x86_64                   57/140 
  Installing       : libtasn1-4.19.0-2.fc38.x86_64                       58/140 
  Installing       : libunistring1.0-1.0-1.fc38.x86_64                   59/140 
  Installing       : libidn2-2.3.4-2.fc38.x86_64                         60/140 
  Installing       : lz4-libs-1.9.4-3.fc39.x86_64                        61/140 
  Installing       : systemd-libs-253.4-1.fc39.x86_64                    62/140 
  Installing       : dbus-libs-1:1.14.6-1.fc38.x86_64                    63/140 
  Installing       : libpsl-0.21.2-2.fc38.x86_64                         64/140 
  Installing       : findutils-1:4.9.0-4.fc39.x86_64                     65/140 
  Installing       : libb2-0.98.1-8.fc38.x86_64                          66/140 
  Installing       : cyrus-sasl-lib-2.1.28-10.fc39.x86_64                67/140 
  Installing       : libcomps-0.1.19-1.fc39.x86_64                       68/140 
  Installing       : grep-3.9-1.fc39.x86_64                              69/140 
  Installing       : libblkid-2.39-0.5.fc39.x86_64                       70/140 
  Installing       : libmount-2.39-0.5.fc39.x86_64                       71/140 
  Installing       : libgcrypt-1.10.2-1.fc39.x86_64                      72/140 
  Installing       : libksba-1.6.3-2.fc38.x86_64                         73/140 
  Installing       : mpfr-4.1.1-3.fc38.x86_64                            74/140 
  Installing       : nettle-3.8-3.fc38.x86_64                            75/140 
  Installing       : elfutils-default-yama-scope-0.189-2.fc39.noarch     76/140 
  Running scriptlet: elfutils-default-yama-scope-0.189-2.fc39.noarch     76/140 
  Installing       : elfutils-libs-0.189-2.fc39.x86_64                   77/140 
  Installing       : alternatives-1.24-1.fc39.x86_64                     78/140 
  Installing       : p11-kit-trust-0.24.1-6.fc38.x86_64                  79/140 
  Running scriptlet: p11-kit-trust-0.24.1-6.fc38.x86_64                  79/140 
  Installing       : libbrotli-1.0.9-11.fc38.x86_64                      80/140 
  Installing       : libcap-ng-0.8.3-5.fc38.x86_64                       81/140 
  Installing       : audit-libs-3.1.1-1.fc39.x86_64                      82/140 
  Installing       : libsemanage-3.5-2.fc39.x86_64                       83/140 
  Installing       : libeconf-0.4.0-5.fc38.x86_64                        84/140 
  Installing       : shadow-utils-2:4.13-6.fc39.x86_64                   85/140 
  Installing       : libnghttp2-1.53.0-1.fc39.x86_64                     86/140 
  Installing       : libsigsegv-2.14-4.fc38.x86_64                       87/140 
  Installing       : gawk-5.1.1-5.fc38.x86_64                            88/140 
  Installing       : libunistring-1.1-3.fc38.x86_64                      89/140 
  Installing       : gnutls-3.8.0-3.fc39.x86_64                          90/140 
  Installing       : glib2-2.76.2-1.fc39.x86_64                          91/140 
  Installing       : libverto-0.3.2-5.fc38.x86_64                        92/140 
  Installing       : libyaml-0.2.5-9.fc38.x86_64                         93/140 
  Installing       : mpdecimal-2.5.1-6.fc38.x86_64                       94/140 
  Installing       : npth-1.6-12.fc38.x86_64                             95/140 
  Installing       : coreutils-common-9.3-1.fc39.x86_64                  96/140 
  Installing       : openssl-libs-1:3.0.8-2.fc39.x86_64                  97/140 
  Installing       : coreutils-9.3-1.fc39.x86_64                         98/140 
  Running scriptlet: ca-certificates-2023.2.60-2.fc38.noarch             99/140 
  Installing       : ca-certificates-2023.2.60-2.fc38.noarch             99/140 
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  Installing       : rpm-sequoia-1.4.0-2.fc39.x86_64                    100/140 
  Installing       : rpm-libs-4.18.1-3.fc39.x86_64                      101/140 
  Installing       : krb5-libs-1.20.1-9.fc39.x86_64                     102/140 
  Installing       : libtirpc-1.3.3-1.rc1.fc39.x86_64                   103/140 
  Installing       : libmodulemd-2.15.0-2.fc39.x86_64                   104/140 
  Installing       : libfsverity-1.4-9.fc38.x86_64                      105/140 
  Installing       : zchunk-libs-1.3.1-1.fc39.x86_64                    106/140 
  Installing       : libsolv-0.7.24-2.fc39.x86_64                       107/140 
  Installing       : libnsl2-2.0.0-5.fc38.x86_64                        108/140 
  Installing       : libssh-0.10.5-1.fc39.x86_64                        109/140 
  Installing       : rpm-build-libs-4.18.1-3.fc39.x86_64                110/140 
  Installing       : python-pip-wheel-23.0.1-2.fc39.noarch              111/140 
  Installing       : python3-3.11.3-1.fc39.x86_64                       112/140 
  Installing       : python3-libs-3.11.3-1.fc39.x86_64                  113/140 
  Installing       : python3-dbus-1.3.2-2.fc38.x86_64                   114/140 
  Installing       : python3-libcomps-0.1.19-1.fc39.x86_64              115/140 
  Installing       : python3-distro-1.8.0-3.fc39.noarch                 116/140 
  Installing       : python3-six-1.16.0-9.fc38.noarch                   117/140 
  Installing       : python3-dateutil-1:2.8.2-6.fc39.noarch             118/140 
  Installing       : python3-systemd-235-2.fc38.x86_64                  119/140 
  Installing       : libarchive-3.6.1-5.fc39.x86_64                     120/140 
  Installing       : libevent-2.1.12-8.fc38.x86_64                      121/140 
  Installing       : openldap-2.6.4-2.fc39.x86_64                       122/140 
  Installing       : libcurl-8.0.1-3.fc39.x86_64                        123/140 
  Installing       : gnupg2-2.4.1-1.fc39.x86_64                         124/140 
  Installing       : gpgme-1.17.1-5.fc39.x86_64                         125/140 
  Installing       : librepo-1.15.1-2.fc38.x86_64                       126/140 
  Installing       : libdnf-0.70.1-1.fc39.x86_64                        127/140 
  Installing       : python3-libdnf-0.70.1-1.fc39.x86_64                128/140 
  Installing       : python3-hawkey-0.70.1-1.fc39.x86_64                129/140 
  Installing       : python3-gpg-1.17.1-5.fc39.x86_64                   130/140 
  Installing       : curl-8.0.1-3.fc39.x86_64                           131/140 
  Running scriptlet: tpm2-tss-4.0.1-3.fc38.x86_64                       132/140 
useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'

  Installing       : tpm2-tss-4.0.1-3.fc38.x86_64                       132/140 
  Installing       : ima-evm-utils-1.4-7.fc38.x86_64                    133/140 
  Installing       : rpm-sign-libs-4.18.1-3.fc39.x86_64                 134/140 
  Installing       : python3-rpm-4.18.1-3.fc39.x86_64                   135/140 
  Installing       : python3-dnf-4.15.0-1.fc39.noarch                   136/140 
  Installing       : python3-dnf-plugins-core-4.4.1-1.fc39.noarch       137/140 
  Installing       : dnf-plugins-core-4.4.1-1.fc39.noarch               138/140 
  Installing       : dnf-4.15.0-1.fc39.noarch                           139/140 
  Running scriptlet: dnf-4.15.0-1.fc39.noarch                           139/140 
  Running scriptlet: rpm-4.18.1-3.fc39.x86_64                           140/140 
  Installing       : rpm-4.18.1-3.fc39.x86_64                           140/140 
  Running scriptlet: filesystem-3.18-4.fc39.x86_64                      140/140 
  Running scriptlet: ca-certificates-2023.2.60-2.fc38.noarch            140/140 
  Running scriptlet: rpm-4.18.1-3.fc39.x86_64                           140/140 
  Verifying        : alternatives-1.24-1.fc39.x86_64                      1/140 
  Verifying        : audit-libs-3.1.1-1.fc39.x86_64                       2/140 
  Verifying        : basesystem-11-15.fc38.noarch                         3/140 
  Verifying        : bash-5.2.15-3.fc38.x86_64                            4/140 
  Verifying        : bzip2-libs-1.0.8-13.fc38.x86_64                      5/140 
  Verifying        : ca-certificates-2023.2.60-2.fc38.noarch              6/140 
  Verifying        : coreutils-9.3-1.fc39.x86_64                          7/140 
  Verifying        : coreutils-common-9.3-1.fc39.x86_64                   8/140 
  Verifying        : crypto-policies-20230420-1.git3d08ae7.fc39.noarc     9/140 
  Verifying        : curl-8.0.1-3.fc39.x86_64                            10/140 
  Verifying        : cyrus-sasl-lib-2.1.28-10.fc39.x86_64                11/140 
  Verifying        : dbus-libs-1:1.14.6-1.fc38.x86_64                    12/140 
  Verifying        : dnf-4.15.0-1.fc39.noarch                            13/140 
  Verifying        : dnf-data-4.15.0-1.fc39.noarch                       14/140 
  Verifying        : dnf-plugins-core-4.4.1-1.fc39.noarch                15/140 
  Verifying        : elfutils-default-yama-scope-0.189-2.fc39.noarch     16/140 
  Verifying        : elfutils-libelf-0.189-2.fc39.x86_64                 17/140 
  Verifying        : elfutils-libs-0.189-2.fc39.x86_64                   18/140 
  Verifying        : expat-2.5.0-2.fc38.x86_64                           19/140 
  Verifying        : fedora-gpg-keys-39-0.1.noarch                       20/140 
  Verifying        : fedora-release-39-0.11.noarch                       21/140 
  Verifying        : fedora-release-common-39-0.11.noarch                22/140 
  Verifying        : fedora-release-identity-basic-39-0.11.noarch        23/140 
  Verifying        : fedora-repos-39-0.1.noarch                          24/140 
  Verifying        : fedora-repos-rawhide-39-0.1.noarch                  25/140 
  Verifying        : file-libs-5.44-3.fc39.x86_64                        26/140 
  Verifying        : filesystem-3.18-4.fc39.x86_64                       27/140 
  Verifying        : findutils-1:4.9.0-4.fc39.x86_64                     28/140 
  Verifying        : gawk-5.1.1-5.fc38.x86_64                            29/140 
  Verifying        : gdbm-libs-1:1.23-3.fc38.x86_64                      30/140 
  Verifying        : glib2-2.76.2-1.fc39.x86_64                          31/140 
  Verifying        : glibc-2.37.9000-9.fc39.x86_64                       32/140 
  Verifying        : glibc-common-2.37.9000-9.fc39.x86_64                33/140 
  Verifying        : glibc-minimal-langpack-2.37.9000-9.fc39.x86_64      34/140 
  Verifying        : gmp-1:6.2.1-4.fc38.x86_64                           35/140 
  Verifying        : gnupg2-2.4.1-1.fc39.x86_64                          36/140 
  Verifying        : gnutls-3.8.0-3.fc39.x86_64                          37/140 
  Verifying        : gpgme-1.17.1-5.fc39.x86_64                          38/140 
  Verifying        : grep-3.9-1.fc39.x86_64                              39/140 
  Verifying        : ima-evm-utils-1.4-7.fc38.x86_64                     40/140 
  Verifying        : json-c-0.16-4.fc38.x86_64                           41/140 
  Verifying        : keyutils-libs-1.6.1-6.fc38.x86_64                   42/140 
  Verifying        : krb5-libs-1.20.1-9.fc39.x86_64                      43/140 
  Verifying        : libacl-2.3.1-7.fc39.x86_64                          44/140 
  Verifying        : libarchive-3.6.1-5.fc39.x86_64                      45/140 
  Verifying        : libassuan-2.5.5-6.fc38.x86_64                       46/140 
  Verifying        : libattr-2.5.1-7.fc39.x86_64                         47/140 
  Verifying        : libb2-0.98.1-8.fc38.x86_64                          48/140 
  Verifying        : libblkid-2.39-0.5.fc39.x86_64                       49/140 
  Verifying        : libbrotli-1.0.9-11.fc38.x86_64                      50/140 
  Verifying        : libcap-2.48-6.fc38.x86_64                           51/140 
  Verifying        : libcap-ng-0.8.3-5.fc38.x86_64                       52/140 
  Verifying        : libcom_err-1.46.5-4.fc38.x86_64                     53/140 
  Verifying        : libcomps-0.1.19-1.fc39.x86_64                       54/140 
  Verifying        : libcurl-8.0.1-3.fc39.x86_64                         55/140 
  Verifying        : libdnf-0.70.1-1.fc39.x86_64                         56/140 
  Verifying        : libeconf-0.4.0-5.fc38.x86_64                        57/140 
  Verifying        : libevent-2.1.12-8.fc38.x86_64                       58/140 
  Verifying        : libffi-3.4.4-2.fc38.x86_64                          59/140 
  Verifying        : libfsverity-1.4-9.fc38.x86_64                       60/140 
  Verifying        : libgcc-13.1.1-2.fc39.x86_64                         61/140 
  Verifying        : libgcrypt-1.10.2-1.fc39.x86_64                      62/140 
  Verifying        : libgomp-13.1.1-2.fc39.x86_64                        63/140 
  Verifying        : libgpg-error-1.47-1.fc39.x86_64                     64/140 
  Verifying        : libidn2-2.3.4-2.fc38.x86_64                         65/140 
  Verifying        : libksba-1.6.3-2.fc38.x86_64                         66/140 
  Verifying        : libmodulemd-2.15.0-2.fc39.x86_64                    67/140 
  Verifying        : libmount-2.39-0.5.fc39.x86_64                       68/140 
  Verifying        : libnghttp2-1.53.0-1.fc39.x86_64                     69/140 
  Verifying        : libnsl2-2.0.0-5.fc38.x86_64                         70/140 
  Verifying        : libpsl-0.21.2-2.fc38.x86_64                         71/140 
  Verifying        : librepo-1.15.1-2.fc38.x86_64                        72/140 
  Verifying        : libreport-filesystem-2.17.10-1.fc39.noarch          73/140 
  Verifying        : libselinux-3.5-1.fc39.x86_64                        74/140 
  Verifying        : libsemanage-3.5-2.fc39.x86_64                       75/140 
  Verifying        : libsepol-3.5-1.fc39.x86_64                          76/140 
  Verifying        : libsigsegv-2.14-4.fc38.x86_64                       77/140 
  Verifying        : libsmartcols-2.39-0.5.fc39.x86_64                   78/140 
  Verifying        : libsolv-0.7.24-2.fc39.x86_64                        79/140 
  Verifying        : libssh-0.10.5-1.fc39.x86_64                         80/140 
  Verifying        : libssh-config-0.10.5-1.fc39.noarch                  81/140 
  Verifying        : libstdc++-13.1.1-2.fc39.x86_64                      82/140 
  Verifying        : libtasn1-4.19.0-2.fc38.x86_64                       83/140 
  Verifying        : libtirpc-1.3.3-1.rc1.fc39.x86_64                    84/140 
  Verifying        : libunistring-1.1-3.fc38.x86_64                      85/140 
  Verifying        : libunistring1.0-1.0-1.fc38.x86_64                   86/140 
  Verifying        : libuuid-2.39-0.5.fc39.x86_64                        87/140 
  Verifying        : libverto-0.3.2-5.fc38.x86_64                        88/140 
  Verifying        : libxcrypt-4.4.33-7.fc39.x86_64                      89/140 
  Verifying        : libxml2-2.10.4-1.fc39.x86_64                        90/140 
  Verifying        : libyaml-0.2.5-9.fc38.x86_64                         91/140 
  Verifying        : libzstd-1.5.5-1.fc39.x86_64                         92/140 
  Verifying        : lua-libs-5.4.4-9.fc39.x86_64                        93/140 
  Verifying        : lz4-libs-1.9.4-3.fc39.x86_64                        94/140 
  Verifying        : mpdecimal-2.5.1-6.fc38.x86_64                       95/140 
  Verifying        : mpfr-4.1.1-3.fc38.x86_64                            96/140 
  Verifying        : ncurses-base-6.4-3.20230114.fc38.noarch             97/140 
  Verifying        : ncurses-libs-6.4-3.20230114.fc38.x86_64             98/140 
  Verifying        : nettle-3.8-3.fc38.x86_64                            99/140 
  Verifying        : npth-1.6-12.fc38.x86_64                            100/140 
  Verifying        : openldap-2.6.4-2.fc39.x86_64                       101/140 
  Verifying        : openssl-libs-1:3.0.8-2.fc39.x86_64                 102/140 
  Verifying        : p11-kit-0.24.1-6.fc38.x86_64                       103/140 
  Verifying        : p11-kit-trust-0.24.1-6.fc38.x86_64                 104/140 
  Verifying        : pcre2-10.42-1.fc38.1.x86_64                        105/140 
  Verifying        : pcre2-syntax-10.42-1.fc38.1.noarch                 106/140 
  Verifying        : popt-1.19-2.fc38.x86_64                            107/140 
  Verifying        : publicsuffix-list-dafsa-20230318-1.fc39.noarch     108/140 
  Verifying        : python-pip-wheel-23.0.1-2.fc39.noarch              109/140 
  Verifying        : python-setuptools-wheel-67.7.2-1.fc39.noarch       110/140 
  Verifying        : python3-3.11.3-1.fc39.x86_64                       111/140 
  Verifying        : python3-dateutil-1:2.8.2-6.fc39.noarch             112/140 
  Verifying        : python3-dbus-1.3.2-2.fc38.x86_64                   113/140 
  Verifying        : python3-distro-1.8.0-3.fc39.noarch                 114/140 
  Verifying        : python3-dnf-4.15.0-1.fc39.noarch                   115/140 
  Verifying        : python3-dnf-plugins-core-4.4.1-1.fc39.noarch       116/140 
  Verifying        : python3-gpg-1.17.1-5.fc39.x86_64                   117/140 
  Verifying        : python3-hawkey-0.70.1-1.fc39.x86_64                118/140 
  Verifying        : python3-libcomps-0.1.19-1.fc39.x86_64              119/140 
  Verifying        : python3-libdnf-0.70.1-1.fc39.x86_64                120/140 
  Verifying        : python3-libs-3.11.3-1.fc39.x86_64                  121/140 
  Verifying        : python3-rpm-4.18.1-3.fc39.x86_64                   122/140 
  Verifying        : python3-six-1.16.0-9.fc38.noarch                   123/140 
  Verifying        : python3-systemd-235-2.fc38.x86_64                  124/140 
  Verifying        : readline-8.2-3.fc38.x86_64                         125/140 
  Verifying        : rpm-4.18.1-3.fc39.x86_64                           126/140 
  Verifying        : rpm-build-libs-4.18.1-3.fc39.x86_64                127/140 
  Verifying        : rpm-libs-4.18.1-3.fc39.x86_64                      128/140 
  Verifying        : rpm-sequoia-1.4.0-2.fc39.x86_64                    129/140 
  Verifying        : rpm-sign-libs-4.18.1-3.fc39.x86_64                 130/140 
  Verifying        : sed-4.8-12.fc38.x86_64                             131/140 
  Verifying        : setup-2.14.3-3.fc39.noarch                         132/140 
  Verifying        : shadow-utils-2:4.13-6.fc39.x86_64                  133/140 
  Verifying        : sqlite-libs-3.41.2-1.fc39.x86_64                   134/140 
  Verifying        : systemd-libs-253.4-1.fc39.x86_64                   135/140 
  Verifying        : tpm2-tss-4.0.1-3.fc38.x86_64                       136/140 
  Verifying        : tzdata-2023c-1.fc39.noarch                         137/140 
  Verifying        : xz-libs-5.4.3-1.fc39.x86_64                        138/140 
  Verifying        : zchunk-libs-1.3.1-1.fc39.x86_64                    139/140 
  Verifying        : zlib-1.2.13-3.fc38.x86_64                          140/140 
Installed products updated.

Installed:
  alternatives-1.24-1.fc39.x86_64                                               
  audit-libs-3.1.1-1.fc39.x86_64                                                
  basesystem-11-15.fc38.noarch                                                  
  bash-5.2.15-3.fc38.x86_64                                                     
  bzip2-libs-1.0.8-13.fc38.x86_64                                               
  ca-certificates-2023.2.60-2.fc38.noarch                                       
  coreutils-9.3-1.fc39.x86_64                                                   
  coreutils-common-9.3-1.fc39.x86_64                                            
  crypto-policies-20230420-1.git3d08ae7.fc39.noarch                             
  curl-8.0.1-3.fc39.x86_64                                                      
  cyrus-sasl-lib-2.1.28-10.fc39.x86_64                                          
  dbus-libs-1:1.14.6-1.fc38.x86_64                                              
  dnf-4.15.0-1.fc39.noarch                                                      
  dnf-data-4.15.0-1.fc39.noarch                                                 
  dnf-plugins-core-4.4.1-1.fc39.noarch                                          
  elfutils-default-yama-scope-0.189-2.fc39.noarch                               
  elfutils-libelf-0.189-2.fc39.x86_64                                           
  elfutils-libs-0.189-2.fc39.x86_64                                             
  expat-2.5.0-2.fc38.x86_64                                                     
  fedora-gpg-keys-39-0.1.noarch                                                 
  fedora-release-39-0.11.noarch                                                 
  fedora-release-common-39-0.11.noarch                                          
  fedora-release-identity-basic-39-0.11.noarch                                  
  fedora-repos-39-0.1.noarch                                                    
  fedora-repos-rawhide-39-0.1.noarch                                            
  file-libs-5.44-3.fc39.x86_64                                                  
  filesystem-3.18-4.fc39.x86_64                                                 
  findutils-1:4.9.0-4.fc39.x86_64                                               
  gawk-5.1.1-5.fc38.x86_64                                                      
  gdbm-libs-1:1.23-3.fc38.x86_64                                                
  glib2-2.76.2-1.fc39.x86_64                                                    
  glibc-2.37.9000-9.fc39.x86_64                                                 
  glibc-common-2.37.9000-9.fc39.x86_64                                          
  glibc-minimal-langpack-2.37.9000-9.fc39.x86_64                                
  gmp-1:6.2.1-4.fc38.x86_64                                                     
  gnupg2-2.4.1-1.fc39.x86_64                                                    
  gnutls-3.8.0-3.fc39.x86_64                                                    
  gpgme-1.17.1-5.fc39.x86_64                                                    
  grep-3.9-1.fc39.x86_64                                                        
  ima-evm-utils-1.4-7.fc38.x86_64                                               
  json-c-0.16-4.fc38.x86_64                                                     
  keyutils-libs-1.6.1-6.fc38.x86_64                                             
  krb5-libs-1.20.1-9.fc39.x86_64                                                
  libacl-2.3.1-7.fc39.x86_64                                                    
  libarchive-3.6.1-5.fc39.x86_64                                                
  libassuan-2.5.5-6.fc38.x86_64                                                 
  libattr-2.5.1-7.fc39.x86_64                                                   
  libb2-0.98.1-8.fc38.x86_64                                                    
  libblkid-2.39-0.5.fc39.x86_64                                                 
  libbrotli-1.0.9-11.fc38.x86_64                                                
  libcap-2.48-6.fc38.x86_64                                                     
  libcap-ng-0.8.3-5.fc38.x86_64                                                 
  libcom_err-1.46.5-4.fc38.x86_64                                               
  libcomps-0.1.19-1.fc39.x86_64                                                 
  libcurl-8.0.1-3.fc39.x86_64                                                   
  libdnf-0.70.1-1.fc39.x86_64                                                   
  libeconf-0.4.0-5.fc38.x86_64                                                  
  libevent-2.1.12-8.fc38.x86_64                                                 
  libffi-3.4.4-2.fc38.x86_64                                                    
  libfsverity-1.4-9.fc38.x86_64                                                 
  libgcc-13.1.1-2.fc39.x86_64                                                   
  libgcrypt-1.10.2-1.fc39.x86_64                                                
  libgomp-13.1.1-2.fc39.x86_64                                                  
  libgpg-error-1.47-1.fc39.x86_64                                               
  libidn2-2.3.4-2.fc38.x86_64                                                   
  libksba-1.6.3-2.fc38.x86_64                                                   
  libmodulemd-2.15.0-2.fc39.x86_64                                              
  libmount-2.39-0.5.fc39.x86_64                                                 
  libnghttp2-1.53.0-1.fc39.x86_64                                               
  libnsl2-2.0.0-5.fc38.x86_64                                                   
  libpsl-0.21.2-2.fc38.x86_64                                                   
  librepo-1.15.1-2.fc38.x86_64                                                  
  libreport-filesystem-2.17.10-1.fc39.noarch                                    
  libselinux-3.5-1.fc39.x86_64                                                  
  libsemanage-3.5-2.fc39.x86_64                                                 
  libsepol-3.5-1.fc39.x86_64                                                    
  libsigsegv-2.14-4.fc38.x86_64                                                 
  libsmartcols-2.39-0.5.fc39.x86_64                                             
  libsolv-0.7.24-2.fc39.x86_64                                                  
  libssh-0.10.5-1.fc39.x86_64                                                   
  libssh-config-0.10.5-1.fc39.noarch                                            
  libstdc++-13.1.1-2.fc39.x86_64                                                
  libtasn1-4.19.0-2.fc38.x86_64                                                 
  libtirpc-1.3.3-1.rc1.fc39.x86_64                                              
  libunistring-1.1-3.fc38.x86_64                                                
  libunistring1.0-1.0-1.fc38.x86_64                                             
  libuuid-2.39-0.5.fc39.x86_64                                                  
  libverto-0.3.2-5.fc38.x86_64                                                  
  libxcrypt-4.4.33-7.fc39.x86_64                                                
  libxml2-2.10.4-1.fc39.x86_64                                                  
  libyaml-0.2.5-9.fc38.x86_64                                                   
  libzstd-1.5.5-1.fc39.x86_64                                                   
  lua-libs-5.4.4-9.fc39.x86_64                                                  
  lz4-libs-1.9.4-3.fc39.x86_64                                                  
  mpdecimal-2.5.1-6.fc38.x86_64                                                 
  mpfr-4.1.1-3.fc38.x86_64                                                      
  ncurses-base-6.4-3.20230114.fc38.noarch                                       
  ncurses-libs-6.4-3.20230114.fc38.x86_64                                       
  nettle-3.8-3.fc38.x86_64                                                      
  npth-1.6-12.fc38.x86_64                                                       
  openldap-2.6.4-2.fc39.x86_64                                                  
  openssl-libs-1:3.0.8-2.fc39.x86_64                                            
  p11-kit-0.24.1-6.fc38.x86_64                                                  
  p11-kit-trust-0.24.1-6.fc38.x86_64                                            
  pcre2-10.42-1.fc38.1.x86_64                                                   
  pcre2-syntax-10.42-1.fc38.1.noarch                                            
  popt-1.19-2.fc38.x86_64                                                       
  publicsuffix-list-dafsa-20230318-1.fc39.noarch                                
  python-pip-wheel-23.0.1-2.fc39.noarch                                         
  python-setuptools-wheel-67.7.2-1.fc39.noarch                                  
  python3-3.11.3-1.fc39.x86_64                                                  
  python3-dateutil-1:2.8.2-6.fc39.noarch                                        
  python3-dbus-1.3.2-2.fc38.x86_64                                              
  python3-distro-1.8.0-3.fc39.noarch                                            
  python3-dnf-4.15.0-1.fc39.noarch                                              
  python3-dnf-plugins-core-4.4.1-1.fc39.noarch                                  
  python3-gpg-1.17.1-5.fc39.x86_64                                              
  python3-hawkey-0.70.1-1.fc39.x86_64                                           
  python3-libcomps-0.1.19-1.fc39.x86_64                                         
  python3-libdnf-0.70.1-1.fc39.x86_64                                           
  python3-libs-3.11.3-1.fc39.x86_64                                             
  python3-rpm-4.18.1-3.fc39.x86_64                                              
  python3-six-1.16.0-9.fc38.noarch                                              
  python3-systemd-235-2.fc38.x86_64                                             
  readline-8.2-3.fc38.x86_64                                                    
  rpm-4.18.1-3.fc39.x86_64                                                      
  rpm-build-libs-4.18.1-3.fc39.x86_64                                           
  rpm-libs-4.18.1-3.fc39.x86_64                                                 
  rpm-sequoia-1.4.0-2.fc39.x86_64                                               
  rpm-sign-libs-4.18.1-3.fc39.x86_64                                            
  sed-4.8-12.fc38.x86_64                                                        
  setup-2.14.3-3.fc39.noarch                                                    
  shadow-utils-2:4.13-6.fc39.x86_64                                             
  sqlite-libs-3.41.2-1.fc39.x86_64                                              
  systemd-libs-253.4-1.fc39.x86_64                                              
  tpm2-tss-4.0.1-3.fc38.x86_64                                                  
  tzdata-2023c-1.fc39.noarch                                                    
  xz-libs-5.4.3-1.fc39.x86_64                                                   
  zchunk-libs-1.3.1-1.fc39.x86_64                                               
  zlib-1.2.13-3.fc38.x86_64                                                     

Complete!
Finish(bootstrap): dnf install
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1684275986.169171/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
Mock Version: 3.5
INFO: Mock Version: 3.5
Start: dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                 2.5 kB/s | 257  B     00:00    
fedora                                          3.3 MB/s |  71 MB     00:21    
Dependencies resolved.
================================================================================
 Package                       Arch   Version                      Repo    Size
================================================================================
Installing group/module packages:
 bash                          x86_64 5.2.15-3.fc38                fedora 1.8 M
 bzip2                         x86_64 1.0.8-13.fc38                fedora  52 k
 coreutils                     x86_64 9.3-1.fc39                   fedora 1.1 M
 cpio                          x86_64 2.13-14.fc38                 fedora 276 k
 diffutils                     x86_64 3.9-4.fc39                   fedora 397 k
 fedora-release-common         noarch 39-0.11                      fedora  22 k
 findutils                     x86_64 1:4.9.0-4.fc39               fedora 491 k
 gawk                          x86_64 5.1.1-5.fc38                 fedora 1.0 M
 glibc-minimal-langpack        x86_64 2.37.9000-9.fc39             fedora  52 k
 grep                          x86_64 3.9-1.fc39                   fedora 295 k
 gzip                          x86_64 1.12-3.fc38                  fedora 166 k
 info                          x86_64 7.0.3-1.fc39                 fedora 184 k
 patch                         x86_64 2.7.6-21.fc39                fedora 126 k
 redhat-rpm-config             noarch 254-1.fc39                   fedora  83 k
 rpm-build                     x86_64 4.18.1-3.fc39                fedora  77 k
 sed                           x86_64 4.8-12.fc38                  fedora 306 k
 shadow-utils                  x86_64 2:4.13-6.fc39                fedora 1.3 M
 tar                           x86_64 2:1.34-8.fc39                fedora 888 k
 unzip                         x86_64 6.0-60.fc38                  fedora 184 k
 util-linux                    x86_64 2.39-0.5.fc39                fedora 2.6 M
 which                         x86_64 2.21-39.fc39                 fedora  42 k
 xz                            x86_64 5.4.3-1.fc39                 fedora 555 k
Installing dependencies:
 alternatives                  x86_64 1.24-1.fc39                  fedora  39 k
 ansible-srpm-macros           noarch 1-10.fc39                    fedora  21 k
 audit-libs                    x86_64 3.1.1-1.fc39                 fedora 117 k
 authselect                    x86_64 1.4.2-2.fc38                 fedora 144 k
 authselect-libs               x86_64 1.4.2-2.fc38                 fedora 249 k
 basesystem                    noarch 11-15.fc38                   fedora 7.0 k
 binutils                      x86_64 2.40-7.fc39                  fedora 5.6 M
 binutils-gold                 x86_64 2.40-7.fc39                  fedora 795 k
 bzip2-libs                    x86_64 1.0.8-13.fc38                fedora  41 k
 ca-certificates               noarch 2023.2.60-2.fc38             fedora 845 k
 coreutils-common              x86_64 9.3-1.fc39                   fedora 2.1 M
 cracklib                      x86_64 2.9.7-31.fc38                fedora  92 k
 crypto-policies               noarch 20230420-1.git3d08ae7.fc39   fedora  94 k
 curl                          x86_64 8.0.1-3.fc39                 fedora 350 k
 cyrus-sasl-lib                x86_64 2.1.28-10.fc39               fedora 792 k
 debugedit                     x86_64 5.0-7.fc38                   fedora  78 k
 dwz                           x86_64 0.15-2.fc38                  fedora 135 k
 ed                            x86_64 1.19-2.fc38                  fedora  78 k
 efi-srpm-macros               noarch 5-7.fc38                     fedora  22 k
 elfutils                      x86_64 0.189-2.fc39                 fedora 536 k
 elfutils-debuginfod-client    x86_64 0.189-2.fc39                 fedora  39 k
 elfutils-default-yama-scope   noarch 0.189-2.fc39                 fedora  15 k
 elfutils-libelf               x86_64 0.189-2.fc39                 fedora 196 k
 elfutils-libs                 x86_64 0.189-2.fc39                 fedora 260 k
 fedora-gpg-keys               noarch 39-0.1                       fedora 126 k
 fedora-release                noarch 39-0.11                      fedora  12 k
 fedora-release-identity-basic noarch 39-0.11                      fedora  13 k
 fedora-repos                  noarch 39-0.1                       fedora 9.4 k
 fedora-repos-rawhide          noarch 39-0.1                       fedora 9.0 k
 file                          x86_64 5.44-3.fc39                  fedora  50 k
 file-libs                     x86_64 5.44-3.fc39                  fedora 730 k
 filesystem                    x86_64 3.18-4.fc39                  fedora 1.1 M
 fonts-srpm-macros             noarch 1:2.0.5-11.fc38              fedora  26 k
 fpc-srpm-macros               noarch 1.3-7.fc38                   fedora 7.8 k
 gdb-minimal                   x86_64 13.1-5.fc39                  fedora 4.2 M
 gdbm-libs                     x86_64 1:1.23-3.fc38                fedora  56 k
 ghc-srpm-macros               noarch 1.6.1-1.fc38                 fedora 8.0 k
 glibc                         x86_64 2.37.9000-9.fc39             fedora 2.1 M
 glibc-common                  x86_64 2.37.9000-9.fc39             fedora 330 k
 glibc-gconv-extra             x86_64 2.37.9000-9.fc39             fedora 1.6 M
 gmp                           x86_64 1:6.2.1-4.fc38               fedora 313 k
 gnat-srpm-macros              noarch 6-2.fc38                     fedora 8.8 k
 go-srpm-macros                noarch 3.2.0-3.fc39                 fedora  27 k
 jansson                       x86_64 2.13.1-6.fc38                fedora  44 k
 kernel-srpm-macros            noarch 1.0-18.fc39                  fedora 9.4 k
 keyutils-libs                 x86_64 1.6.1-6.fc38                 fedora  31 k
 krb5-libs                     x86_64 1.20.1-9.fc39                fedora 727 k
 libacl                        x86_64 2.3.1-7.fc39                 fedora  23 k
 libarchive                    x86_64 3.6.1-5.fc39                 fedora 400 k
 libattr                       x86_64 2.5.1-7.fc39                 fedora  18 k
 libblkid                      x86_64 2.39-0.5.fc39                fedora 116 k
 libbrotli                     x86_64 1.0.9-11.fc38                fedora 317 k
 libcap                        x86_64 2.48-6.fc38                  fedora  67 k
 libcap-ng                     x86_64 0.8.3-5.fc38                 fedora  32 k
 libcom_err                    x86_64 1.46.5-4.fc38                fedora  26 k
 libcurl                       x86_64 8.0.1-3.fc39                 fedora 313 k
 libdb                         x86_64 5.3.28-55.fc38               fedora 758 k
 libeconf                      x86_64 0.4.0-5.fc38                 fedora  27 k
 libevent                      x86_64 2.1.12-8.fc38                fedora 257 k
 libfdisk                      x86_64 2.39-0.5.fc39                fedora 162 k
 libffi                        x86_64 3.4.4-2.fc38                 fedora  38 k
 libgcc                        x86_64 13.1.1-2.fc39                fedora 106 k
 libgomp                       x86_64 13.1.1-2.fc39                fedora 316 k
 libidn2                       x86_64 2.3.4-2.fc38                 fedora 160 k
 libmount                      x86_64 2.39-0.5.fc39                fedora 153 k
 libnghttp2                    x86_64 1.53.0-1.fc39                fedora  75 k
 libnsl2                       x86_64 2.0.0-5.fc38                 fedora  30 k
 libpkgconf                    x86_64 1.9.4-2.fc39                 fedora  38 k
 libpsl                        x86_64 0.21.2-2.fc38                fedora  65 k
 libpwquality                  x86_64 1.4.5-3.fc38                 fedora 119 k
 libselinux                    x86_64 3.5-1.fc39                   fedora  87 k
 libsemanage                   x86_64 3.5-2.fc39                   fedora 120 k
 libsepol                      x86_64 3.5-1.fc39                   fedora 324 k
 libsigsegv                    x86_64 2.14-4.fc38                  fedora  27 k
 libsmartcols                  x86_64 2.39-0.5.fc39                fedora  67 k
 libssh                        x86_64 0.10.5-1.fc39                fedora 211 k
 libssh-config                 noarch 0.10.5-1.fc39                fedora 9.0 k
 libstdc++                     x86_64 13.1.1-2.fc39                fedora 860 k
 libtasn1                      x86_64 4.19.0-2.fc38                fedora  74 k
 libtirpc                      x86_64 1.3.3-1.rc1.fc39             fedora  93 k
 libunistring1.0               x86_64 1.0-1.fc38                   fedora 539 k
 libutempter                   x86_64 1.2.1-9.fc39                 fedora  26 k
 libuuid                       x86_64 2.39-0.5.fc39                fedora  28 k
 libverto                      x86_64 0.3.2-5.fc38                 fedora  21 k
 libxcrypt                     x86_64 4.4.33-7.fc39                fedora 120 k
 libxml2                       x86_64 2.10.4-1.fc39                fedora 700 k
 libzstd                       x86_64 1.5.5-1.fc39                 fedora 308 k
 lua-libs                      x86_64 5.4.4-9.fc39                 fedora 133 k
 lua-srpm-macros               noarch 1-8.fc38                     fedora 8.6 k
 lz4-libs                      x86_64 1.9.4-3.fc39                 fedora  67 k
 mpfr                          x86_64 4.1.1-3.fc38                 fedora 600 k
 ncurses-base                  noarch 6.4-3.20230114.fc38          fedora  87 k
 ncurses-libs                  x86_64 6.4-3.20230114.fc38          fedora 333 k
 ocaml-srpm-macros             noarch 7-3.fc38                     fedora  13 k
 openblas-srpm-macros          noarch 2-13.fc38                    fedora 7.5 k
 openldap                      x86_64 2.6.4-2.fc39                 fedora 255 k
 openssl-libs                  x86_64 1:3.0.8-2.fc39               fedora 2.1 M
 p11-kit                       x86_64 0.24.1-6.fc38                fedora 359 k
 p11-kit-trust                 x86_64 0.24.1-6.fc38                fedora 136 k
 package-notes-srpm-macros     noarch 0.5-7.fc38                   fedora  11 k
 pam                           x86_64 1.5.2-19.fc39                fedora 532 k
 pam-libs                      x86_64 1.5.2-19.fc39                fedora  57 k
 pcre2                         x86_64 10.42-1.fc38.1               fedora 234 k
 pcre2-syntax                  noarch 10.42-1.fc38.1               fedora 144 k
 perl-srpm-macros              noarch 1-48.fc38                    fedora 8.4 k
 pkgconf                       x86_64 1.9.4-2.fc39                 fedora  42 k
 pkgconf-m4                    noarch 1.9.4-2.fc39                 fedora  14 k
 pkgconf-pkg-config            x86_64 1.9.4-2.fc39                 fedora 9.5 k
 popt                          x86_64 1.19-2.fc38                  fedora  67 k
 publicsuffix-list-dafsa       noarch 20230318-1.fc39              fedora  60 k
 pyproject-srpm-macros         noarch 1.7.0-1.fc39                 fedora  14 k
 python-srpm-macros            noarch 3.11-10.fc39                 fedora  26 k
 qt5-srpm-macros               noarch 5.15.9-1.fc39                fedora 8.1 k
 readline                      x86_64 8.2-3.fc38                   fedora 212 k
 rpm                           x86_64 4.18.1-3.fc39                fedora 571 k
 rpm-build-libs                x86_64 4.18.1-3.fc39                fedora  94 k
 rpm-libs                      x86_64 4.18.1-3.fc39                fedora 312 k
 rpm-sequoia                   x86_64 1.4.0-2.fc39                 fedora 849 k
 rpmautospec-rpm-macros        noarch 0.3.5-1.fc38                 fedora 9.3 k
 rust-srpm-macros              noarch 24-1.fc39                    fedora  12 k
 setup                         noarch 2.14.3-3.fc39                fedora 152 k
 sqlite-libs                   x86_64 3.41.2-1.fc39                fedora 669 k
 systemd-libs                  x86_64 253.4-1.fc39                 fedora 652 k
 tzdata                        noarch 2023c-1.fc39                 fedora 718 k
 util-linux-core               x86_64 2.39-0.5.fc39                fedora 484 k
 xxhash-libs                   x86_64 0.8.1-4.fc38                 fedora  40 k
 xz-libs                       x86_64 5.4.3-1.fc39                 fedora 108 k
 zip                           x86_64 3.0-36.fc38                  fedora 265 k
 zlib                          x86_64 1.2.13-3.fc38                fedora  95 k
 zstd                          x86_64 1.5.5-1.fc39                 fedora 482 k
Installing Groups:
 Buildsystem building group                                                    

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

Total download size: 54 M
Installed size: 188 M
Downloading Packages:
(1/152): ansible-srpm-macros-1-10.fc39.noarch.r 168 kB/s |  21 kB     00:00    
(2/152): alternatives-1.24-1.fc39.x86_64.rpm    274 kB/s |  39 kB     00:00    
(3/152): audit-libs-3.1.1-1.fc39.x86_64.rpm     768 kB/s | 117 kB     00:00    
(4/152): authselect-1.4.2-2.fc38.x86_64.rpm     2.3 MB/s | 144 kB     00:00    
(5/152): authselect-libs-1.4.2-2.fc38.x86_64.rp 4.2 MB/s | 249 kB     00:00    
(6/152): basesystem-11-15.fc38.noarch.rpm       139 kB/s | 7.0 kB     00:00    
(7/152): bash-5.2.15-3.fc38.x86_64.rpm           27 MB/s | 1.8 MB     00:00    
(8/152): bzip2-1.0.8-13.fc38.x86_64.rpm         968 kB/s |  52 kB     00:00    
(9/152): binutils-2.40-7.fc39.x86_64.rpm         39 MB/s | 5.6 MB     00:00    
(10/152): binutils-gold-2.40-7.fc39.x86_64.rpm  5.3 MB/s | 795 kB     00:00    
(11/152): bzip2-libs-1.0.8-13.fc38.x86_64.rpm   962 kB/s |  41 kB     00:00    
(12/152): ca-certificates-2023.2.60-2.fc38.noar  29 MB/s | 845 kB     00:00    
(13/152): coreutils-9.3-1.fc39.x86_64.rpm        28 MB/s | 1.1 MB     00:00    
(14/152): coreutils-common-9.3-1.fc39.x86_64.rp  31 MB/s | 2.1 MB     00:00    
(15/152): cpio-2.13-14.fc38.x86_64.rpm          6.1 MB/s | 276 kB     00:00    
(16/152): cracklib-2.9.7-31.fc38.x86_64.rpm     3.0 MB/s |  92 kB     00:00    
(17/152): crypto-policies-20230420-1.git3d08ae7 4.4 MB/s |  94 kB     00:00    
(18/152): curl-8.0.1-3.fc39.x86_64.rpm           14 MB/s | 350 kB     00:00    
(19/152): cyrus-sasl-lib-2.1.28-10.fc39.x86_64.  24 MB/s | 792 kB     00:00    
(20/152): debugedit-5.0-7.fc38.x86_64.rpm       2.1 MB/s |  78 kB     00:00    
(21/152): diffutils-3.9-4.fc39.x86_64.rpm       9.2 MB/s | 397 kB     00:00    
(22/152): dwz-0.15-2.fc38.x86_64.rpm            3.5 MB/s | 135 kB     00:00    
(23/152): ed-1.19-2.fc38.x86_64.rpm             3.4 MB/s |  78 kB     00:00    
(24/152): efi-srpm-macros-5-7.fc38.noarch.rpm   1.0 MB/s |  22 kB     00:00    
(25/152): elfutils-0.189-2.fc39.x86_64.rpm       15 MB/s | 536 kB     00:00    
(26/152): elfutils-debuginfod-client-0.189-2.fc 1.5 MB/s |  39 kB     00:00    
(27/152): elfutils-default-yama-scope-0.189-2.f 752 kB/s |  15 kB     00:00    
(28/152): elfutils-libelf-0.189-2.fc39.x86_64.r 8.8 MB/s | 196 kB     00:00    
(29/152): elfutils-libs-0.189-2.fc39.x86_64.rpm  10 MB/s | 260 kB     00:00    
(30/152): fedora-gpg-keys-39-0.1.noarch.rpm     5.1 MB/s | 126 kB     00:00    
(31/152): fedora-release-39-0.11.noarch.rpm     620 kB/s |  12 kB     00:00    
(32/152): fedora-release-common-39-0.11.noarch. 1.1 MB/s |  22 kB     00:00    
(33/152): fedora-release-identity-basic-39-0.11 656 kB/s |  13 kB     00:00    
(34/152): fedora-repos-39-0.1.noarch.rpm        471 kB/s | 9.4 kB     00:00    
(35/152): fedora-repos-rawhide-39-0.1.noarch.rp 457 kB/s | 9.0 kB     00:00    
(36/152): file-5.44-3.fc39.x86_64.rpm           1.0 MB/s |  50 kB     00:00    
(37/152): file-libs-5.44-3.fc39.x86_64.rpm       19 MB/s | 730 kB     00:00    
(38/152): filesystem-3.18-4.fc39.x86_64.rpm      22 MB/s | 1.1 MB     00:00    
(39/152): findutils-4.9.0-4.fc39.x86_64.rpm      19 MB/s | 491 kB     00:00    
(40/152): fonts-srpm-macros-2.0.5-11.fc38.noarc 511 kB/s |  26 kB     00:00    
(41/152): fpc-srpm-macros-1.3-7.fc38.noarch.rpm 117 kB/s | 7.8 kB     00:00    
(42/152): gawk-5.1.1-5.fc38.x86_64.rpm           14 MB/s | 1.0 MB     00:00    
(43/152): gdb-minimal-13.1-5.fc39.x86_64.rpm     25 MB/s | 4.2 MB     00:00    
(44/152): gdbm-libs-1.23-3.fc38.x86_64.rpm      414 kB/s |  56 kB     00:00    
(45/152): ghc-srpm-macros-1.6.1-1.fc38.noarch.r  63 kB/s | 8.0 kB     00:00    
(46/152): glibc-2.37.9000-9.fc39.x86_64.rpm      41 MB/s | 2.1 MB     00:00    
(47/152): glibc-common-2.37.9000-9.fc39.x86_64. 6.1 MB/s | 330 kB     00:00    
(48/152): glibc-gconv-extra-2.37.9000-9.fc39.x8  17 MB/s | 1.6 MB     00:00    
(49/152): glibc-minimal-langpack-2.37.9000-9.fc 1.1 MB/s |  52 kB     00:00    
(50/152): gmp-6.2.1-4.fc38.x86_64.rpm           7.0 MB/s | 313 kB     00:00    
(51/152): gnat-srpm-macros-6-2.fc38.noarch.rpm  405 kB/s | 8.8 kB     00:00    
(52/152): go-srpm-macros-3.2.0-3.fc39.noarch.rp 1.1 MB/s |  27 kB     00:00    
(53/152): grep-3.9-1.fc39.x86_64.rpm             11 MB/s | 295 kB     00:00    
(54/152): gzip-1.12-3.fc38.x86_64.rpm           3.3 MB/s | 166 kB     00:00    
(55/152): info-7.0.3-1.fc39.x86_64.rpm          2.8 MB/s | 184 kB     00:00    
(56/152): jansson-2.13.1-6.fc38.x86_64.rpm      379 kB/s |  44 kB     00:00    
(57/152): kernel-srpm-macros-1.0-18.fc39.noarch 100 kB/s | 9.4 kB     00:00    
(58/152): keyutils-libs-1.6.1-6.fc38.x86_64.rpm 405 kB/s |  31 kB     00:00    
(59/152): krb5-libs-1.20.1-9.fc39.x86_64.rpm     25 MB/s | 727 kB     00:00    
(60/152): libacl-2.3.1-7.fc39.x86_64.rpm        1.1 MB/s |  23 kB     00:00    
(61/152): libarchive-3.6.1-5.fc39.x86_64.rpm     16 MB/s | 400 kB     00:00    
(62/152): libattr-2.5.1-7.fc39.x86_64.rpm       822 kB/s |  18 kB     00:00    
(63/152): libblkid-2.39-0.5.fc39.x86_64.rpm     5.0 MB/s | 116 kB     00:00    
(64/152): libbrotli-1.0.9-11.fc38.x86_64.rpm     12 MB/s | 317 kB     00:00    
(65/152): libcap-2.48-6.fc38.x86_64.rpm         2.8 MB/s |  67 kB     00:00    
(66/152): libcap-ng-0.8.3-5.fc38.x86_64.rpm     1.6 MB/s |  32 kB     00:00    
(67/152): libcom_err-1.46.5-4.fc38.x86_64.rpm   1.3 MB/s |  26 kB     00:00    
(68/152): libcurl-8.0.1-3.fc39.x86_64.rpm        13 MB/s | 313 kB     00:00    
(69/152): libdb-5.3.28-55.fc38.x86_64.rpm        14 MB/s | 758 kB     00:00    
(70/152): libeconf-0.4.0-5.fc38.x86_64.rpm      601 kB/s |  27 kB     00:00    
(71/152): libevent-2.1.12-8.fc38.x86_64.rpm     6.2 MB/s | 257 kB     00:00    
(72/152): libfdisk-2.39-0.5.fc39.x86_64.rpm     3.3 MB/s | 162 kB     00:00    
(73/152): libffi-3.4.4-2.fc38.x86_64.rpm        791 kB/s |  38 kB     00:00    
(74/152): libgcc-13.1.1-2.fc39.x86_64.rpm       2.2 MB/s | 106 kB     00:00    
(75/152): libgomp-13.1.1-2.fc39.x86_64.rpm       13 MB/s | 316 kB     00:00    
(76/152): libidn2-2.3.4-2.fc38.x86_64.rpm       6.6 MB/s | 160 kB     00:00    
(77/152): libmount-2.39-0.5.fc39.x86_64.rpm     6.2 MB/s | 153 kB     00:00    
(78/152): libnghttp2-1.53.0-1.fc39.x86_64.rpm   3.6 MB/s |  75 kB     00:00    
(79/152): libnsl2-2.0.0-5.fc38.x86_64.rpm       1.5 MB/s |  30 kB     00:00    
(80/152): libpkgconf-1.9.4-2.fc39.x86_64.rpm    873 kB/s |  38 kB     00:00    
(81/152): libpsl-0.21.2-2.fc38.x86_64.rpm       2.5 MB/s |  65 kB     00:00    
(82/152): libpwquality-1.4.5-3.fc38.x86_64.rpm  3.1 MB/s | 119 kB     00:00    
(83/152): libselinux-3.5-1.fc39.x86_64.rpm      4.2 MB/s |  87 kB     00:00    
(84/152): libsemanage-3.5-2.fc39.x86_64.rpm     5.6 MB/s | 120 kB     00:00    
(85/152): libsepol-3.5-1.fc39.x86_64.rpm         14 MB/s | 324 kB     00:00    
(86/152): libsigsegv-2.14-4.fc38.x86_64.rpm     1.3 MB/s |  27 kB     00:00    
(87/152): libsmartcols-2.39-0.5.fc39.x86_64.rpm 3.3 MB/s |  67 kB     00:00    
(88/152): libssh-0.10.5-1.fc39.x86_64.rpm       9.2 MB/s | 211 kB     00:00    
(89/152): libssh-config-0.10.5-1.fc39.noarch.rp 459 kB/s | 9.0 kB     00:00    
(90/152): libstdc++-13.1.1-2.fc39.x86_64.rpm     29 MB/s | 860 kB     00:00    
(91/152): libtasn1-4.19.0-2.fc38.x86_64.rpm     3.5 MB/s |  74 kB     00:00    
(92/152): libtirpc-1.3.3-1.rc1.fc39.x86_64.rpm  4.3 MB/s |  93 kB     00:00    
(93/152): libunistring1.0-1.0-1.fc38.x86_64.rpm  21 MB/s | 539 kB     00:00    
(94/152): libutempter-1.2.1-9.fc39.x86_64.rpm   787 kB/s |  26 kB     00:00    
(95/152): libuuid-2.39-0.5.fc39.x86_64.rpm      859 kB/s |  28 kB     00:00    
(96/152): libverto-0.3.2-5.fc38.x86_64.rpm      1.0 MB/s |  21 kB     00:00    
(97/152): libxcrypt-4.4.33-7.fc39.x86_64.rpm    5.4 MB/s | 120 kB     00:00    
(98/152): libxml2-2.10.4-1.fc39.x86_64.rpm       21 MB/s | 700 kB     00:00    
(99/152): libzstd-1.5.5-1.fc39.x86_64.rpm       5.5 MB/s | 308 kB     00:00    
(100/152): lua-libs-5.4.4-9.fc39.x86_64.rpm     3.7 MB/s | 133 kB     00:00    
(101/152): lua-srpm-macros-1-8.fc38.noarch.rpm  359 kB/s | 8.6 kB     00:00    
(102/152): lz4-libs-1.9.4-3.fc39.x86_64.rpm     3.2 MB/s |  67 kB     00:00    
(103/152): mpfr-4.1.1-3.fc38.x86_64.rpm          21 MB/s | 600 kB     00:00    
(104/152): ncurses-base-6.4-3.20230114.fc38.noa 2.9 MB/s |  87 kB     00:00    
(105/152): ncurses-libs-6.4-3.20230114.fc38.x86  14 MB/s | 333 kB     00:00    
(106/152): ocaml-srpm-macros-7-3.fc38.noarch.rp 633 kB/s |  13 kB     00:00    
(107/152): openblas-srpm-macros-2-13.fc38.noarc 342 kB/s | 7.5 kB     00:00    
(108/152): openldap-2.6.4-2.fc39.x86_64.rpm      11 MB/s | 255 kB     00:00    
(109/152): openssl-libs-3.0.8-2.fc39.x86_64.rpm  33 MB/s | 2.1 MB     00:00    
(110/152): p11-kit-0.24.1-6.fc38.x86_64.rpm     5.3 MB/s | 359 kB     00:00    
(111/152): p11-kit-trust-0.24.1-6.fc38.x86_64.r 2.6 MB/s | 136 kB     00:00    
(112/152): package-notes-srpm-macros-0.5-7.fc38 512 kB/s |  11 kB     00:00    
(113/152): pam-1.5.2-19.fc39.x86_64.rpm         5.7 MB/s | 532 kB     00:00    
(114/152): pam-libs-1.5.2-19.fc39.x86_64.rpm    620 kB/s |  57 kB     00:00    
(115/152): patch-2.7.6-21.fc39.x86_64.rpm       1.5 MB/s | 126 kB     00:00    
(116/152): pcre2-10.42-1.fc38.1.x86_64.rpm       10 MB/s | 234 kB     00:00    
(117/152): pcre2-syntax-10.42-1.fc38.1.noarch.r 6.7 MB/s | 144 kB     00:00    
(118/152): perl-srpm-macros-1-48.fc38.noarch.rp 393 kB/s | 8.4 kB     00:00    
(119/152): pkgconf-1.9.4-2.fc39.x86_64.rpm      1.4 MB/s |  42 kB     00:00    
(120/152): pkgconf-m4-1.9.4-2.fc39.noarch.rpm   235 kB/s |  14 kB     00:00    
(121/152): pkgconf-pkg-config-1.9.4-2.fc39.x86_ 134 kB/s | 9.5 kB     00:00    
(122/152): popt-1.19-2.fc38.x86_64.rpm          1.4 MB/s |  67 kB     00:00    
(123/152): publicsuffix-list-dafsa-20230318-1.f 2.9 MB/s |  60 kB     00:00    
(124/152): pyproject-srpm-macros-1.7.0-1.fc39.n 539 kB/s |  14 kB     00:00    
(125/152): python-srpm-macros-3.11-10.fc39.noar 905 kB/s |  26 kB     00:00    
(126/152): qt5-srpm-macros-5.15.9-1.fc39.noarch 299 kB/s | 8.1 kB     00:00    
(127/152): readline-8.2-3.fc38.x86_64.rpm       9.1 MB/s | 212 kB     00:00    
(128/152): redhat-rpm-config-254-1.fc39.noarch. 3.5 MB/s |  83 kB     00:00    
(129/152): rpm-4.18.1-3.fc39.x86_64.rpm          19 MB/s | 571 kB     00:00    
(130/152): rpm-build-4.18.1-3.fc39.x86_64.rpm   3.3 MB/s |  77 kB     00:00    
(131/152): rpm-build-libs-4.18.1-3.fc39.x86_64. 4.3 MB/s |  94 kB     00:00    
(132/152): rpm-libs-4.18.1-3.fc39.x86_64.rpm     13 MB/s | 312 kB     00:00    
(133/152): rpm-sequoia-1.4.0-2.fc39.x86_64.rpm   27 MB/s | 849 kB     00:00    
(134/152): rpmautospec-rpm-macros-0.3.5-1.fc38. 204 kB/s | 9.3 kB     00:00    
(135/152): rust-srpm-macros-24-1.fc39.noarch.rp 335 kB/s |  12 kB     00:00    
(136/152): sed-4.8-12.fc38.x86_64.rpm           8.2 MB/s | 306 kB     00:00    
(137/152): setup-2.14.3-3.fc39.noarch.rpm       6.9 MB/s | 152 kB     00:00    
(138/152): shadow-utils-4.13-6.fc39.x86_64.rpm   28 MB/s | 1.3 MB     00:00    
(139/152): sqlite-libs-3.41.2-1.fc39.x86_64.rpm  16 MB/s | 669 kB     00:00    
(140/152): systemd-libs-253.4-1.fc39.x86_64.rpm  13 MB/s | 652 kB     00:00    
(141/152): tar-1.34-8.fc39.x86_64.rpm            15 MB/s | 888 kB     00:00    
(142/152): tzdata-2023c-1.fc39.noarch.rpm        14 MB/s | 718 kB     00:00    
(143/152): unzip-6.0-60.fc38.x86_64.rpm         3.6 MB/s | 184 kB     00:00    
(144/152): util-linux-2.39-0.5.fc39.x86_64.rpm   20 MB/s | 2.6 MB     00:00    
(145/152): util-linux-core-2.39-0.5.fc39.x86_64 4.0 MB/s | 484 kB     00:00    
(146/152): which-2.21-39.fc39.x86_64.rpm        383 kB/s |  42 kB     00:00    
(147/152): xxhash-libs-0.8.1-4.fc38.x86_64.rpm  631 kB/s |  40 kB     00:00    
(148/152): xz-5.4.3-1.fc39.x86_64.rpm           5.9 MB/s | 555 kB     00:00    
(149/152): xz-libs-5.4.3-1.fc39.x86_64.rpm      1.1 MB/s | 108 kB     00:00    
(150/152): zip-3.0-36.fc38.x86_64.rpm           2.3 MB/s | 265 kB     00:00    
(151/152): zlib-1.2.13-3.fc38.x86_64.rpm        987 kB/s |  95 kB     00:00    
(152/152): zstd-1.5.5-1.fc39.x86_64.rpm         941 kB/s | 482 kB     00:00    
--------------------------------------------------------------------------------
Total                                            19 MB/s |  54 MB     00:02     
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0x18B8E74C:
 Userid     : "Fedora (39) <fedora-39-primary@fedoraproject.org>"
 Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary
Key imported successfully
fedora                                          1.6 MB/s | 1.6 kB     00:00    
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary (0x18B8E74C) is already installed
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0xEB10B464:
 Userid     : "Fedora (38) <fedora-38-primary@fedoraproject.org>"
 Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.18-4.fc39.x86_64                          1/1 
  Preparing        :                                                        1/1 
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  Installing       : tzdata-2023c-1.fc39.noarch                           3/152 
  Installing       : fedora-release-identity-basic-39-0.11.noarch         4/152 
  Installing       : rust-srpm-macros-24-1.fc39.noarch                    5/152 
  Installing       : qt5-srpm-macros-5.15.9-1.fc39.noarch                 6/152 
  Installing       : pyproject-srpm-macros-1.7.0-1.fc39.noarch            7/152 
  Installing       : publicsuffix-list-dafsa-20230318-1.fc39.noarch       8/152 
  Installing       : pkgconf-m4-1.9.4-2.fc39.noarch                       9/152 
  Installing       : perl-srpm-macros-1-48.fc38.noarch                   10/152 
  Installing       : pcre2-syntax-10.42-1.fc38.1.noarch                  11/152 
  Installing       : package-notes-srpm-macros-0.5-7.fc38.noarch         12/152 
  Installing       : openblas-srpm-macros-2-13.fc38.noarch               13/152 
  Installing       : ocaml-srpm-macros-7-3.fc38.noarch                   14/152 
  Installing       : ncurses-base-6.4-3.20230114.fc38.noarch             15/152 
  Installing       : libssh-config-0.10.5-1.fc39.noarch                  16/152 
  Installing       : kernel-srpm-macros-1.0-18.fc39.noarch               17/152 
  Installing       : gnat-srpm-macros-6-2.fc38.noarch                    18/152 
  Installing       : ghc-srpm-macros-1.6.1-1.fc38.noarch                 19/152 
  Installing       : fpc-srpm-macros-1.3-7.fc38.noarch                   20/152 
  Installing       : fedora-gpg-keys-39-0.1.noarch                       21/152 
  Installing       : fedora-release-39-0.11.noarch                       22/152 
  Installing       : fedora-release-common-39-0.11.noarch                23/152 
  Installing       : fedora-repos-rawhide-39-0.1.noarch                  24/152 
  Installing       : fedora-repos-39-0.1.noarch                          25/152 
  Installing       : setup-2.14.3-3.fc39.noarch                          26/152 
warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.14.3-3.fc39.noarch                          26/152 
  Installing       : filesystem-3.18-4.fc39.x86_64                       27/152 
  Installing       : basesystem-11-15.fc38.noarch                        28/152 
  Installing       : glibc-gconv-extra-2.37.9000-9.fc39.x86_64           29/152 
  Running scriptlet: glibc-gconv-extra-2.37.9000-9.fc39.x86_64           29/152 
  Installing       : glibc-minimal-langpack-2.37.9000-9.fc39.x86_64      30/152 
  Installing       : glibc-common-2.37.9000-9.fc39.x86_64                31/152 
  Running scriptlet: glibc-2.37.9000-9.fc39.x86_64                       32/152 
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  Installing       : ncurses-libs-6.4-3.20230114.fc38.x86_64             33/152 
  Installing       : bash-5.2.15-3.fc38.x86_64                           34/152 
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  Installing       : zlib-1.2.13-3.fc38.x86_64                           35/152 
  Installing       : xz-libs-5.4.3-1.fc39.x86_64                         36/152 
  Installing       : bzip2-libs-1.0.8-13.fc38.x86_64                     37/152 
  Installing       : libzstd-1.5.5-1.fc39.x86_64                         38/152 
  Installing       : elfutils-libelf-0.189-2.fc39.x86_64                 39/152 
  Installing       : libstdc++-13.1.1-2.fc39.x86_64                      40/152 
  Installing       : libuuid-2.39-0.5.fc39.x86_64                        41/152 
  Installing       : popt-1.19-2.fc38.x86_64                             42/152 
  Installing       : libblkid-2.39-0.5.fc39.x86_64                       43/152 
  Installing       : readline-8.2-3.fc38.x86_64                          44/152 
  Installing       : gmp-1:6.2.1-4.fc38.x86_64                           45/152 
  Installing       : libattr-2.5.1-7.fc39.x86_64                         46/152 
  Installing       : libacl-2.3.1-7.fc39.x86_64                          47/152 
  Installing       : libcap-2.48-6.fc38.x86_64                           48/152 
  Installing       : libxcrypt-4.4.33-7.fc39.x86_64                      49/152 
  Installing       : libeconf-0.4.0-5.fc38.x86_64                        50/152 
  Installing       : lz4-libs-1.9.4-3.fc39.x86_64                        51/152 
  Installing       : systemd-libs-253.4-1.fc39.x86_64                    52/152 
  Installing       : mpfr-4.1.1-3.fc38.x86_64                            53/152 
  Installing       : dwz-0.15-2.fc38.x86_64                              54/152 
  Installing       : unzip-6.0-60.fc38.x86_64                            55/152 
  Installing       : file-libs-5.44-3.fc39.x86_64                        56/152 
  Installing       : file-5.44-3.fc39.x86_64                             57/152 
  Installing       : sqlite-libs-3.41.2-1.fc39.x86_64                    58/152 
  Installing       : alternatives-1.24-1.fc39.x86_64                     59/152 
  Installing       : jansson-2.13.1-6.fc38.x86_64                        60/152 
  Installing       : libcap-ng-0.8.3-5.fc38.x86_64                       61/152 
  Installing       : audit-libs-3.1.1-1.fc39.x86_64                      62/152 
  Installing       : pam-libs-1.5.2-19.fc39.x86_64                       63/152 
  Installing       : libcom_err-1.46.5-4.fc38.x86_64                     64/152 
  Installing       : libsepol-3.5-1.fc39.x86_64                          65/152 
  Installing       : libsmartcols-2.39-0.5.fc39.x86_64                   66/152 
  Installing       : libunistring1.0-1.0-1.fc38.x86_64                   67/152 
  Installing       : libidn2-2.3.4-2.fc38.x86_64                         68/152 
  Installing       : lua-libs-5.4.4-9.fc39.x86_64                        69/152 
  Installing       : pcre2-10.42-1.fc38.1.x86_64                         70/152 
  Installing       : libselinux-3.5-1.fc39.x86_64                        71/152 
  Installing       : sed-4.8-12.fc38.x86_64                              72/152 
  Installing       : grep-3.9-1.fc39.x86_64                              73/152 
  Installing       : findutils-1:4.9.0-4.fc39.x86_64                     74/152 
  Installing       : xz-5.4.3-1.fc39.x86_64                              75/152 
  Installing       : libmount-2.39-0.5.fc39.x86_64                       76/152 
  Installing       : util-linux-core-2.39-0.5.fc39.x86_64                77/152 
  Installing       : libsemanage-3.5-2.fc39.x86_64                       78/152 
  Installing       : shadow-utils-2:4.13-6.fc39.x86_64                   79/152 
  Running scriptlet: libutempter-1.2.1-9.fc39.x86_64                     80/152 
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  Installing       : tar-2:1.34-8.fc39.x86_64                            81/152 
  Installing       : libpsl-0.21.2-2.fc38.x86_64                         82/152 
  Installing       : zip-3.0-36.fc38.x86_64                              83/152 
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  Installing       : ed-1.19-2.fc38.x86_64                               88/152 
  Installing       : patch-2.7.6-21.fc39.x86_64                          89/152 
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  Installing       : cpio-2.13-14.fc38.x86_64                            91/152 
  Installing       : diffutils-3.9-4.fc39.x86_64                         92/152 
  Installing       : gdbm-libs-1:1.23-3.fc38.x86_64                      93/152 
  Installing       : cyrus-sasl-lib-2.1.28-10.fc39.x86_64                94/152 
  Installing       : keyutils-libs-1.6.1-6.fc38.x86_64                   95/152 
  Installing       : libbrotli-1.0.9-11.fc38.x86_64                      96/152 
  Installing       : libdb-5.3.28-55.fc38.x86_64                         97/152 
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  Installing       : libgomp-13.1.1-2.fc39.x86_64                       100/152 
  Installing       : libnghttp2-1.53.0-1.fc39.x86_64                    101/152 
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  Installing       : libsigsegv-2.14-4.fc38.x86_64                      105/152 
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  Installing       : libtasn1-4.19.0-2.fc38.x86_64                      107/152 
  Installing       : p11-kit-trust-0.24.1-6.fc38.x86_64                 108/152 
  Running scriptlet: p11-kit-trust-0.24.1-6.fc38.x86_64                 108/152 
  Installing       : libverto-0.3.2-5.fc38.x86_64                       109/152 
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  Installing       : coreutils-common-9.3-1.fc39.x86_64                 111/152 
  Installing       : openssl-libs-1:3.0.8-2.fc39.x86_64                 112/152 
  Installing       : coreutils-9.3-1.fc39.x86_64                        113/152 
  Running scriptlet: ca-certificates-2023.2.60-2.fc38.noarch            114/152 
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  Installing       : krb5-libs-1.20.1-9.fc39.x86_64                     115/152 
  Installing       : libtirpc-1.3.3-1.rc1.fc39.x86_64                   116/152 
  Running scriptlet: authselect-libs-1.4.2-2.fc38.x86_64                117/152 
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  Installing       : gzip-1.12-3.fc38.x86_64                            118/152 
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  Installing       : cracklib-2.9.7-31.fc38.x86_64                      121/152 
  Installing       : libpwquality-1.4.5-3.fc38.x86_64                   122/152 
  Installing       : authselect-1.4.2-2.fc38.x86_64                     123/152 
  Installing       : libnsl2-2.0.0-5.fc38.x86_64                        124/152 
  Installing       : pam-1.5.2-19.fc39.x86_64                           125/152 
  Installing       : libssh-0.10.5-1.fc39.x86_64                        126/152 
  Installing       : libarchive-3.6.1-5.fc39.x86_64                     127/152 
  Installing       : libevent-2.1.12-8.fc38.x86_64                      128/152 
  Installing       : openldap-2.6.4-2.fc39.x86_64                       129/152 
  Installing       : libcurl-8.0.1-3.fc39.x86_64                        130/152 
  Installing       : elfutils-libs-0.189-2.fc39.x86_64                  131/152 
  Installing       : elfutils-debuginfod-client-0.189-2.fc39.x86_64     132/152 
  Installing       : binutils-gold-2.40-7.fc39.x86_64                   133/152 
  Installing       : binutils-2.40-7.fc39.x86_64                        134/152 
  Running scriptlet: binutils-2.40-7.fc39.x86_64                        134/152 
  Installing       : elfutils-0.189-2.fc39.x86_64                       135/152 
  Installing       : gdb-minimal-13.1-5.fc39.x86_64                     136/152 
  Installing       : debugedit-5.0-7.fc38.x86_64                        137/152 
  Installing       : rpm-build-libs-4.18.1-3.fc39.x86_64                138/152 
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  Installing       : efi-srpm-macros-5-7.fc38.noarch                    141/152 
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  Installing       : rpmautospec-rpm-macros-0.3.5-1.fc38.noarch         143/152 
  Installing       : ansible-srpm-macros-1-10.fc39.noarch               144/152 
  Installing       : fonts-srpm-macros-1:2.0.5-11.fc38.noarch           145/152 
  Installing       : go-srpm-macros-3.2.0-3.fc39.noarch                 146/152 
  Installing       : python-srpm-macros-3.11-10.fc39.noarch             147/152 
  Installing       : redhat-rpm-config-254-1.fc39.noarch                148/152 
  Installing       : rpm-build-4.18.1-3.fc39.x86_64                     149/152 
  Installing       : util-linux-2.39-0.5.fc39.x86_64                    150/152 
  Installing       : which-2.21-39.fc39.x86_64                          151/152 
  Installing       : info-7.0.3-1.fc39.x86_64                           152/152 
  Running scriptlet: filesystem-3.18-4.fc39.x86_64                      152/152 
  Running scriptlet: ca-certificates-2023.2.60-2.fc38.noarch            152/152 
  Running scriptlet: authselect-libs-1.4.2-2.fc38.x86_64                152/152 
  Running scriptlet: rpm-4.18.1-3.fc39.x86_64                           152/152 
  Running scriptlet: info-7.0.3-1.fc39.x86_64                           152/152 
  Verifying        : alternatives-1.24-1.fc39.x86_64                      1/152 
  Verifying        : ansible-srpm-macros-1-10.fc39.noarch                 2/152 
  Verifying        : audit-libs-3.1.1-1.fc39.x86_64                       3/152 
  Verifying        : authselect-1.4.2-2.fc38.x86_64                       4/152 
  Verifying        : authselect-libs-1.4.2-2.fc38.x86_64                  5/152 
  Verifying        : basesystem-11-15.fc38.noarch                         6/152 
  Verifying        : bash-5.2.15-3.fc38.x86_64                            7/152 
  Verifying        : binutils-2.40-7.fc39.x86_64                          8/152 
  Verifying        : binutils-gold-2.40-7.fc39.x86_64                     9/152 
  Verifying        : bzip2-1.0.8-13.fc38.x86_64                          10/152 
  Verifying        : bzip2-libs-1.0.8-13.fc38.x86_64                     11/152 
  Verifying        : ca-certificates-2023.2.60-2.fc38.noarch             12/152 
  Verifying        : coreutils-9.3-1.fc39.x86_64                         13/152 
  Verifying        : coreutils-common-9.3-1.fc39.x86_64                  14/152 
  Verifying        : cpio-2.13-14.fc38.x86_64                            15/152 
  Verifying        : cracklib-2.9.7-31.fc38.x86_64                       16/152 
  Verifying        : crypto-policies-20230420-1.git3d08ae7.fc39.noarc    17/152 
  Verifying        : curl-8.0.1-3.fc39.x86_64                            18/152 
  Verifying        : cyrus-sasl-lib-2.1.28-10.fc39.x86_64                19/152 
  Verifying        : debugedit-5.0-7.fc38.x86_64                         20/152 
  Verifying        : diffutils-3.9-4.fc39.x86_64                         21/152 
  Verifying        : dwz-0.15-2.fc38.x86_64                              22/152 
  Verifying        : ed-1.19-2.fc38.x86_64                               23/152 
  Verifying        : efi-srpm-macros-5-7.fc38.noarch                     24/152 
  Verifying        : elfutils-0.189-2.fc39.x86_64                        25/152 
  Verifying        : elfutils-debuginfod-client-0.189-2.fc39.x86_64      26/152 
  Verifying        : elfutils-default-yama-scope-0.189-2.fc39.noarch     27/152 
  Verifying        : elfutils-libelf-0.189-2.fc39.x86_64                 28/152 
  Verifying        : elfutils-libs-0.189-2.fc39.x86_64                   29/152 
  Verifying        : fedora-gpg-keys-39-0.1.noarch                       30/152 
  Verifying        : fedora-release-39-0.11.noarch                       31/152 
  Verifying        : fedora-release-common-39-0.11.noarch                32/152 
  Verifying        : fedora-release-identity-basic-39-0.11.noarch        33/152 
  Verifying        : fedora-repos-39-0.1.noarch                          34/152 
  Verifying        : fedora-repos-rawhide-39-0.1.noarch                  35/152 
  Verifying        : file-5.44-3.fc39.x86_64                             36/152 
  Verifying        : file-libs-5.44-3.fc39.x86_64                        37/152 
  Verifying        : filesystem-3.18-4.fc39.x86_64                       38/152 
  Verifying        : findutils-1:4.9.0-4.fc39.x86_64                     39/152 
  Verifying        : fonts-srpm-macros-1:2.0.5-11.fc38.noarch            40/152 
  Verifying        : fpc-srpm-macros-1.3-7.fc38.noarch                   41/152 
  Verifying        : gawk-5.1.1-5.fc38.x86_64                            42/152 
  Verifying        : gdb-minimal-13.1-5.fc39.x86_64                      43/152 
  Verifying        : gdbm-libs-1:1.23-3.fc38.x86_64                      44/152 
  Verifying        : ghc-srpm-macros-1.6.1-1.fc38.noarch                 45/152 
  Verifying        : glibc-2.37.9000-9.fc39.x86_64                       46/152 
  Verifying        : glibc-common-2.37.9000-9.fc39.x86_64                47/152 
  Verifying        : glibc-gconv-extra-2.37.9000-9.fc39.x86_64           48/152 
  Verifying        : glibc-minimal-langpack-2.37.9000-9.fc39.x86_64      49/152 
  Verifying        : gmp-1:6.2.1-4.fc38.x86_64                           50/152 
  Verifying        : gnat-srpm-macros-6-2.fc38.noarch                    51/152 
  Verifying        : go-srpm-macros-3.2.0-3.fc39.noarch                  52/152 
  Verifying        : grep-3.9-1.fc39.x86_64                              53/152 
  Verifying        : gzip-1.12-3.fc38.x86_64                             54/152 
  Verifying        : info-7.0.3-1.fc39.x86_64                            55/152 
  Verifying        : jansson-2.13.1-6.fc38.x86_64                        56/152 
  Verifying        : kernel-srpm-macros-1.0-18.fc39.noarch               57/152 
  Verifying        : keyutils-libs-1.6.1-6.fc38.x86_64                   58/152 
  Verifying        : krb5-libs-1.20.1-9.fc39.x86_64                      59/152 
  Verifying        : libacl-2.3.1-7.fc39.x86_64                          60/152 
  Verifying        : libarchive-3.6.1-5.fc39.x86_64                      61/152 
  Verifying        : libattr-2.5.1-7.fc39.x86_64                         62/152 
  Verifying        : libblkid-2.39-0.5.fc39.x86_64                       63/152 
  Verifying        : libbrotli-1.0.9-11.fc38.x86_64                      64/152 
  Verifying        : libcap-2.48-6.fc38.x86_64                           65/152 
  Verifying        : libcap-ng-0.8.3-5.fc38.x86_64                       66/152 
  Verifying        : libcom_err-1.46.5-4.fc38.x86_64                     67/152 
  Verifying        : libcurl-8.0.1-3.fc39.x86_64                         68/152 
  Verifying        : libdb-5.3.28-55.fc38.x86_64                         69/152 
  Verifying        : libeconf-0.4.0-5.fc38.x86_64                        70/152 
  Verifying        : libevent-2.1.12-8.fc38.x86_64                       71/152 
  Verifying        : libfdisk-2.39-0.5.fc39.x86_64                       72/152 
  Verifying        : libffi-3.4.4-2.fc38.x86_64                          73/152 
  Verifying        : libgcc-13.1.1-2.fc39.x86_64                         74/152 
  Verifying        : libgomp-13.1.1-2.fc39.x86_64                        75/152 
  Verifying        : libidn2-2.3.4-2.fc38.x86_64                         76/152 
  Verifying        : libmount-2.39-0.5.fc39.x86_64                       77/152 
  Verifying        : libnghttp2-1.53.0-1.fc39.x86_64                     78/152 
  Verifying        : libnsl2-2.0.0-5.fc38.x86_64                         79/152 
  Verifying        : libpkgconf-1.9.4-2.fc39.x86_64                      80/152 
  Verifying        : libpsl-0.21.2-2.fc38.x86_64                         81/152 
  Verifying        : libpwquality-1.4.5-3.fc38.x86_64                    82/152 
  Verifying        : libselinux-3.5-1.fc39.x86_64                        83/152 
  Verifying        : libsemanage-3.5-2.fc39.x86_64                       84/152 
  Verifying        : libsepol-3.5-1.fc39.x86_64                          85/152 
  Verifying        : libsigsegv-2.14-4.fc38.x86_64                       86/152 
  Verifying        : libsmartcols-2.39-0.5.fc39.x86_64                   87/152 
  Verifying        : libssh-0.10.5-1.fc39.x86_64                         88/152 
  Verifying        : libssh-config-0.10.5-1.fc39.noarch                  89/152 
  Verifying        : libstdc++-13.1.1-2.fc39.x86_64                      90/152 
  Verifying        : libtasn1-4.19.0-2.fc38.x86_64                       91/152 
  Verifying        : libtirpc-1.3.3-1.rc1.fc39.x86_64                    92/152 
  Verifying        : libunistring1.0-1.0-1.fc38.x86_64                   93/152 
  Verifying        : libutempter-1.2.1-9.fc39.x86_64                     94/152 
  Verifying        : libuuid-2.39-0.5.fc39.x86_64                        95/152 
  Verifying        : libverto-0.3.2-5.fc38.x86_64                        96/152 
  Verifying        : libxcrypt-4.4.33-7.fc39.x86_64                      97/152 
  Verifying        : libxml2-2.10.4-1.fc39.x86_64                        98/152 
  Verifying        : libzstd-1.5.5-1.fc39.x86_64                         99/152 
  Verifying        : lua-libs-5.4.4-9.fc39.x86_64                       100/152 
  Verifying        : lua-srpm-macros-1-8.fc38.noarch                    101/152 
  Verifying        : lz4-libs-1.9.4-3.fc39.x86_64                       102/152 
  Verifying        : mpfr-4.1.1-3.fc38.x86_64                           103/152 
  Verifying        : ncurses-base-6.4-3.20230114.fc38.noarch            104/152 
  Verifying        : ncurses-libs-6.4-3.20230114.fc38.x86_64            105/152 
  Verifying        : ocaml-srpm-macros-7-3.fc38.noarch                  106/152 
  Verifying        : openblas-srpm-macros-2-13.fc38.noarch              107/152 
  Verifying        : openldap-2.6.4-2.fc39.x86_64                       108/152 
  Verifying        : openssl-libs-1:3.0.8-2.fc39.x86_64                 109/152 
  Verifying        : p11-kit-0.24.1-6.fc38.x86_64                       110/152 
  Verifying        : p11-kit-trust-0.24.1-6.fc38.x86_64                 111/152 
  Verifying        : package-notes-srpm-macros-0.5-7.fc38.noarch        112/152 
  Verifying        : pam-1.5.2-19.fc39.x86_64                           113/152 
  Verifying        : pam-libs-1.5.2-19.fc39.x86_64                      114/152 
  Verifying        : patch-2.7.6-21.fc39.x86_64                         115/152 
  Verifying        : pcre2-10.42-1.fc38.1.x86_64                        116/152 
  Verifying        : pcre2-syntax-10.42-1.fc38.1.noarch                 117/152 
  Verifying        : perl-srpm-macros-1-48.fc38.noarch                  118/152 
  Verifying        : pkgconf-1.9.4-2.fc39.x86_64                        119/152 
  Verifying        : pkgconf-m4-1.9.4-2.fc39.noarch                     120/152 
  Verifying        : pkgconf-pkg-config-1.9.4-2.fc39.x86_64             121/152 
  Verifying        : popt-1.19-2.fc38.x86_64                            122/152 
  Verifying        : publicsuffix-list-dafsa-20230318-1.fc39.noarch     123/152 
  Verifying        : pyproject-srpm-macros-1.7.0-1.fc39.noarch          124/152 
  Verifying        : python-srpm-macros-3.11-10.fc39.noarch             125/152 
  Verifying        : qt5-srpm-macros-5.15.9-1.fc39.noarch               126/152 
  Verifying        : readline-8.2-3.fc38.x86_64                         127/152 
  Verifying        : redhat-rpm-config-254-1.fc39.noarch                128/152 
  Verifying        : rpm-4.18.1-3.fc39.x86_64                           129/152 
  Verifying        : rpm-build-4.18.1-3.fc39.x86_64                     130/152 
  Verifying        : rpm-build-libs-4.18.1-3.fc39.x86_64                131/152 
  Verifying        : rpm-libs-4.18.1-3.fc39.x86_64                      132/152 
  Verifying        : rpm-sequoia-1.4.0-2.fc39.x86_64                    133/152 
  Verifying        : rpmautospec-rpm-macros-0.3.5-1.fc38.noarch         134/152 
  Verifying        : rust-srpm-macros-24-1.fc39.noarch                  135/152 
  Verifying        : sed-4.8-12.fc38.x86_64                             136/152 
  Verifying        : setup-2.14.3-3.fc39.noarch                         137/152 
  Verifying        : shadow-utils-2:4.13-6.fc39.x86_64                  138/152 
  Verifying        : sqlite-libs-3.41.2-1.fc39.x86_64                   139/152 
  Verifying        : systemd-libs-253.4-1.fc39.x86_64                   140/152 
  Verifying        : tar-2:1.34-8.fc39.x86_64                           141/152 
  Verifying        : tzdata-2023c-1.fc39.noarch                         142/152 
  Verifying        : unzip-6.0-60.fc38.x86_64                           143/152 
  Verifying        : util-linux-2.39-0.5.fc39.x86_64                    144/152 
  Verifying        : util-linux-core-2.39-0.5.fc39.x86_64               145/152 
  Verifying        : which-2.21-39.fc39.x86_64                          146/152 
  Verifying        : xxhash-libs-0.8.1-4.fc38.x86_64                    147/152 
  Verifying        : xz-5.4.3-1.fc39.x86_64                             148/152 
  Verifying        : xz-libs-5.4.3-1.fc39.x86_64                        149/152 
  Verifying        : zip-3.0-36.fc38.x86_64                             150/152 
  Verifying        : zlib-1.2.13-3.fc38.x86_64                          151/152 
  Verifying        : zstd-1.5.5-1.fc39.x86_64                           152/152 

Installed:
  alternatives-1.24-1.fc39.x86_64                                               
  ansible-srpm-macros-1-10.fc39.noarch                                          
  audit-libs-3.1.1-1.fc39.x86_64                                                
  authselect-1.4.2-2.fc38.x86_64                                                
  authselect-libs-1.4.2-2.fc38.x86_64                                           
  basesystem-11-15.fc38.noarch                                                  
  bash-5.2.15-3.fc38.x86_64                                                     
  binutils-2.40-7.fc39.x86_64                                                   
  binutils-gold-2.40-7.fc39.x86_64                                              
  bzip2-1.0.8-13.fc38.x86_64                                                    
  bzip2-libs-1.0.8-13.fc38.x86_64                                               
  ca-certificates-2023.2.60-2.fc38.noarch                                       
  coreutils-9.3-1.fc39.x86_64                                                   
  coreutils-common-9.3-1.fc39.x86_64                                            
  cpio-2.13-14.fc38.x86_64                                                      
  cracklib-2.9.7-31.fc38.x86_64                                                 
  crypto-policies-20230420-1.git3d08ae7.fc39.noarch                             
  curl-8.0.1-3.fc39.x86_64                                                      
  cyrus-sasl-lib-2.1.28-10.fc39.x86_64                                          
  debugedit-5.0-7.fc38.x86_64                                                   
  diffutils-3.9-4.fc39.x86_64                                                   
  dwz-0.15-2.fc38.x86_64                                                        
  ed-1.19-2.fc38.x86_64                                                         
  efi-srpm-macros-5-7.fc38.noarch                                               
  elfutils-0.189-2.fc39.x86_64                                                  
  elfutils-debuginfod-client-0.189-2.fc39.x86_64                                
  elfutils-default-yama-scope-0.189-2.fc39.noarch                               
  elfutils-libelf-0.189-2.fc39.x86_64                                           
  elfutils-libs-0.189-2.fc39.x86_64                                             
  fedora-gpg-keys-39-0.1.noarch                                                 
  fedora-release-39-0.11.noarch                                                 
  fedora-release-common-39-0.11.noarch                                          
  fedora-release-identity-basic-39-0.11.noarch                                  
  fedora-repos-39-0.1.noarch                                                    
  fedora-repos-rawhide-39-0.1.noarch                                            
  file-5.44-3.fc39.x86_64                                                       
  file-libs-5.44-3.fc39.x86_64                                                  
  filesystem-3.18-4.fc39.x86_64                                                 
  findutils-1:4.9.0-4.fc39.x86_64                                               
  fonts-srpm-macros-1:2.0.5-11.fc38.noarch                                      
  fpc-srpm-macros-1.3-7.fc38.noarch                                             
  gawk-5.1.1-5.fc38.x86_64                                                      
  gdb-minimal-13.1-5.fc39.x86_64                                                
  gdbm-libs-1:1.23-3.fc38.x86_64                                                
  ghc-srpm-macros-1.6.1-1.fc38.noarch                                           
  glibc-2.37.9000-9.fc39.x86_64                                                 
  glibc-common-2.37.9000-9.fc39.x86_64                                          
  glibc-gconv-extra-2.37.9000-9.fc39.x86_64                                     
  glibc-minimal-langpack-2.37.9000-9.fc39.x86_64                                
  gmp-1:6.2.1-4.fc38.x86_64                                                     
  gnat-srpm-macros-6-2.fc38.noarch                                              
  go-srpm-macros-3.2.0-3.fc39.noarch                                            
  grep-3.9-1.fc39.x86_64                                                        
  gzip-1.12-3.fc38.x86_64                                                       
  info-7.0.3-1.fc39.x86_64                                                      
  jansson-2.13.1-6.fc38.x86_64                                                  
  kernel-srpm-macros-1.0-18.fc39.noarch                                         
  keyutils-libs-1.6.1-6.fc38.x86_64                                             
  krb5-libs-1.20.1-9.fc39.x86_64                                                
  libacl-2.3.1-7.fc39.x86_64                                                    
  libarchive-3.6.1-5.fc39.x86_64                                                
  libattr-2.5.1-7.fc39.x86_64                                                   
  libblkid-2.39-0.5.fc39.x86_64                                                 
  libbrotli-1.0.9-11.fc38.x86_64                                                
  libcap-2.48-6.fc38.x86_64                                                     
  libcap-ng-0.8.3-5.fc38.x86_64                                                 
  libcom_err-1.46.5-4.fc38.x86_64                                               
  libcurl-8.0.1-3.fc39.x86_64                                                   
  libdb-5.3.28-55.fc38.x86_64                                                   
  libeconf-0.4.0-5.fc38.x86_64                                                  
  libevent-2.1.12-8.fc38.x86_64                                                 
  libfdisk-2.39-0.5.fc39.x86_64                                                 
  libffi-3.4.4-2.fc38.x86_64                                                    
  libgcc-13.1.1-2.fc39.x86_64                                                   
  libgomp-13.1.1-2.fc39.x86_64                                                  
  libidn2-2.3.4-2.fc38.x86_64                                                   
  libmount-2.39-0.5.fc39.x86_64                                                 
  libnghttp2-1.53.0-1.fc39.x86_64                                               
  libnsl2-2.0.0-5.fc38.x86_64                                                   
  libpkgconf-1.9.4-2.fc39.x86_64                                                
  libpsl-0.21.2-2.fc38.x86_64                                                   
  libpwquality-1.4.5-3.fc38.x86_64                                              
  libselinux-3.5-1.fc39.x86_64                                                  
  libsemanage-3.5-2.fc39.x86_64                                                 
  libsepol-3.5-1.fc39.x86_64                                                    
  libsigsegv-2.14-4.fc38.x86_64                                                 
  libsmartcols-2.39-0.5.fc39.x86_64                                             
  libssh-0.10.5-1.fc39.x86_64                                                   
  libssh-config-0.10.5-1.fc39.noarch                                            
  libstdc++-13.1.1-2.fc39.x86_64                                                
  libtasn1-4.19.0-2.fc38.x86_64                                                 
  libtirpc-1.3.3-1.rc1.fc39.x86_64                                              
  libunistring1.0-1.0-1.fc38.x86_64                                             
  libutempter-1.2.1-9.fc39.x86_64                                               
  libuuid-2.39-0.5.fc39.x86_64                                                  
  libverto-0.3.2-5.fc38.x86_64                                                  
  libxcrypt-4.4.33-7.fc39.x86_64                                                
  libxml2-2.10.4-1.fc39.x86_64                                                  
  libzstd-1.5.5-1.fc39.x86_64                                                   
  lua-libs-5.4.4-9.fc39.x86_64                                                  
  lua-srpm-macros-1-8.fc38.noarch                                               
  lz4-libs-1.9.4-3.fc39.x86_64                                                  
  mpfr-4.1.1-3.fc38.x86_64                                                      
  ncurses-base-6.4-3.20230114.fc38.noarch                                       
  ncurses-libs-6.4-3.20230114.fc38.x86_64                                       
  ocaml-srpm-macros-7-3.fc38.noarch                                             
  openblas-srpm-macros-2-13.fc38.noarch                                         
  openldap-2.6.4-2.fc39.x86_64                                                  
  openssl-libs-1:3.0.8-2.fc39.x86_64                                            
  p11-kit-0.24.1-6.fc38.x86_64                                                  
  p11-kit-trust-0.24.1-6.fc38.x86_64                                            
  package-notes-srpm-macros-0.5-7.fc38.noarch                                   
  pam-1.5.2-19.fc39.x86_64                                                      
  pam-libs-1.5.2-19.fc39.x86_64                                                 
  patch-2.7.6-21.fc39.x86_64                                                    
  pcre2-10.42-1.fc38.1.x86_64                                                   
  pcre2-syntax-10.42-1.fc38.1.noarch                                            
  perl-srpm-macros-1-48.fc38.noarch                                             
  pkgconf-1.9.4-2.fc39.x86_64                                                   
  pkgconf-m4-1.9.4-2.fc39.noarch                                                
  pkgconf-pkg-config-1.9.4-2.fc39.x86_64                                        
  popt-1.19-2.fc38.x86_64                                                       
  publicsuffix-list-dafsa-20230318-1.fc39.noarch                                
  pyproject-srpm-macros-1.7.0-1.fc39.noarch                                     
  python-srpm-macros-3.11-10.fc39.noarch                                        
  qt5-srpm-macros-5.15.9-1.fc39.noarch                                          
  readline-8.2-3.fc38.x86_64                                                    
  redhat-rpm-config-254-1.fc39.noarch                                           
  rpm-4.18.1-3.fc39.x86_64                                                      
  rpm-build-4.18.1-3.fc39.x86_64                                                
  rpm-build-libs-4.18.1-3.fc39.x86_64                                           
  rpm-libs-4.18.1-3.fc39.x86_64                                                 
  rpm-sequoia-1.4.0-2.fc39.x86_64                                               
  rpmautospec-rpm-macros-0.3.5-1.fc38.noarch                                    
  rust-srpm-macros-24-1.fc39.noarch                                             
  sed-4.8-12.fc38.x86_64                                                        
  setup-2.14.3-3.fc39.noarch                                                    
  shadow-utils-2:4.13-6.fc39.x86_64                                             
  sqlite-libs-3.41.2-1.fc39.x86_64                                              
  systemd-libs-253.4-1.fc39.x86_64                                              
  tar-2:1.34-8.fc39.x86_64                                                      
  tzdata-2023c-1.fc39.noarch                                                    
  unzip-6.0-60.fc38.x86_64                                                      
  util-linux-2.39-0.5.fc39.x86_64                                               
  util-linux-core-2.39-0.5.fc39.x86_64                                          
  which-2.21-39.fc39.x86_64                                                     
  xxhash-libs-0.8.1-4.fc38.x86_64                                               
  xz-5.4.3-1.fc39.x86_64                                                        
  xz-libs-5.4.3-1.fc39.x86_64                                                   
  zip-3.0-36.fc38.x86_64                                                        
  zlib-1.2.13-3.fc38.x86_64                                                     
  zstd-1.5.5-1.fc39.x86_64                                                      

Complete!
Finish: dnf install
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: ncurses-base-6.4-3.20230114.fc38.noarch
libsemanage-3.5-2.fc39.x86_64
go-srpm-macros-3.2.0-3.fc39.noarch
shadow-utils-4.13-6.fc39.x86_64
libssh-0.10.5-1.fc39.x86_64
bash-5.2.15-3.fc38.x86_64
libsmartcols-2.39-0.5.fc39.x86_64
elfutils-debuginfod-client-0.189-2.fc39.x86_64
libblkid-2.39-0.5.fc39.x86_64
libbrotli-1.0.9-11.fc38.x86_64
libzstd-1.5.5-1.fc39.x86_64
coreutils-common-9.3-1.fc39.x86_64
glibc-common-2.37.9000-9.fc39.x86_64
kernel-srpm-macros-1.0-18.fc39.noarch
cracklib-2.9.7-31.fc38.x86_64
zip-3.0-36.fc38.x86_64
perl-srpm-macros-1-48.fc38.noarch
gdbm-libs-1.23-3.fc38.x86_64
p11-kit-0.24.1-6.fc38.x86_64
libsepol-3.5-1.fc39.x86_64
readline-8.2-3.fc38.x86_64
grep-3.9-1.fc39.x86_64
glibc-gconv-extra-2.37.9000-9.fc39.x86_64
filesystem-3.18-4.fc39.x86_64
file-5.44-3.fc39.x86_64
libevent-2.1.12-8.fc38.x86_64
efi-srpm-macros-5-7.fc38.noarch
util-linux-2.39-0.5.fc39.x86_64
libfdisk-2.39-0.5.fc39.x86_64
libpkgconf-1.9.4-2.fc39.x86_64
patch-2.7.6-21.fc39.x86_64
fonts-srpm-macros-2.0.5-11.fc38.noarch
libpsl-0.21.2-2.fc38.x86_64
xz-libs-5.4.3-1.fc39.x86_64
libgcc-13.1.1-2.fc39.x86_64
python-srpm-macros-3.11-10.fc39.noarch
zlib-1.2.13-3.fc38.x86_64
sqlite-libs-3.41.2-1.fc39.x86_64
gnat-srpm-macros-6-2.fc38.noarch
xxhash-libs-0.8.1-4.fc38.x86_64
libcurl-8.0.1-3.fc39.x86_64
gawk-5.1.1-5.fc38.x86_64
elfutils-0.189-2.fc39.x86_64
fedora-repos-39-0.1.noarch
tzdata-2023c-1.fc39.noarch
authselect-libs-1.4.2-2.fc38.x86_64
gdb-minimal-13.1-5.fc39.x86_64
cyrus-sasl-lib-2.1.28-10.fc39.x86_64
libsigsegv-2.14-4.fc38.x86_64
diffutils-3.9-4.fc39.x86_64
openldap-2.6.4-2.fc39.x86_64
libcap-ng-0.8.3-5.fc38.x86_64
which-2.21-39.fc39.x86_64
elfutils-libelf-0.189-2.fc39.x86_64
libselinux-3.5-1.fc39.x86_64
lz4-libs-1.9.4-3.fc39.x86_64
rpm-4.18.1-3.fc39.x86_64
fedora-gpg-keys-39-0.1.noarch
libtirpc-1.3.3-1.rc1.fc39.x86_64
bzip2-libs-1.0.8-13.fc38.x86_64
unzip-6.0-60.fc38.x86_64
glibc-minimal-langpack-2.37.9000-9.fc39.x86_64
gpg-pubkey-eb10b464-6202d9c6
dwz-0.15-2.fc38.x86_64
rust-srpm-macros-24-1.fc39.noarch
curl-8.0.1-3.fc39.x86_64
basesystem-11-15.fc38.noarch
file-libs-5.44-3.fc39.x86_64
libstdc++-13.1.1-2.fc39.x86_64
lua-libs-5.4.4-9.fc39.x86_64
gzip-1.12-3.fc38.x86_64
p11-kit-trust-0.24.1-6.fc38.x86_64
krb5-libs-1.20.1-9.fc39.x86_64
libarchive-3.6.1-5.fc39.x86_64
libattr-2.5.1-7.fc39.x86_64
pkgconf-1.9.4-2.fc39.x86_64
pcre2-10.42-1.fc38.1.x86_64
libnsl2-2.0.0-5.fc38.x86_64
zstd-1.5.5-1.fc39.x86_64
qt5-srpm-macros-5.15.9-1.fc39.noarch
libnghttp2-1.53.0-1.fc39.x86_64
libutempter-1.2.1-9.fc39.x86_64
fedora-release-common-39-0.11.noarch
gmp-6.2.1-4.fc38.x86_64
coreutils-9.3-1.fc39.x86_64
package-notes-srpm-macros-0.5-7.fc38.noarch
ghc-srpm-macros-1.6.1-1.fc38.noarch
fedora-repos-rawhide-39-0.1.noarch
pyproject-srpm-macros-1.7.0-1.fc39.noarch
setup-2.14.3-3.fc39.noarch
rpm-build-4.18.1-3.fc39.x86_64
ed-1.19-2.fc38.x86_64
pam-1.5.2-19.fc39.x86_64
libacl-2.3.1-7.fc39.x86_64
libssh-config-0.10.5-1.fc39.noarch
binutils-2.40-7.fc39.x86_64
lua-srpm-macros-1-8.fc38.noarch
fpc-srpm-macros-1.3-7.fc38.noarch
ocaml-srpm-macros-7-3.fc38.noarch
libcom_err-1.46.5-4.fc38.x86_64
audit-libs-3.1.1-1.fc39.x86_64
debugedit-5.0-7.fc38.x86_64
findutils-4.9.0-4.fc39.x86_64
jansson-2.13.1-6.fc38.x86_64
fedora-release-identity-basic-39-0.11.noarch
libcap-2.48-6.fc38.x86_64
pcre2-syntax-10.42-1.fc38.1.noarch
alternatives-1.24-1.fc39.x86_64
libffi-3.4.4-2.fc38.x86_64
ca-certificates-2023.2.60-2.fc38.noarch
redhat-rpm-config-254-1.fc39.noarch
libxcrypt-4.4.33-7.fc39.x86_64
rpm-build-libs-4.18.1-3.fc39.x86_64
info-7.0.3-1.fc39.x86_64
openblas-srpm-macros-2-13.fc38.noarch
libdb-5.3.28-55.fc38.x86_64
libtasn1-4.19.0-2.fc38.x86_64
keyutils-libs-1.6.1-6.fc38.x86_64
libuuid-2.39-0.5.fc39.x86_64
xz-5.4.3-1.fc39.x86_64
pkgconf-m4-1.9.4-2.fc39.noarch
libunistring1.0-1.0-1.fc38.x86_64
libxml2-2.10.4-1.fc39.x86_64
elfutils-libs-0.189-2.fc39.x86_64
libpwquality-1.4.5-3.fc38.x86_64
mpfr-4.1.1-3.fc38.x86_64
systemd-libs-253.4-1.fc39.x86_64
pam-libs-1.5.2-19.fc39.x86_64
authselect-1.4.2-2.fc38.x86_64
ncurses-libs-6.4-3.20230114.fc38.x86_64
libidn2-2.3.4-2.fc38.x86_64
tar-1.34-8.fc39.x86_64
cpio-2.13-14.fc38.x86_64
rpm-libs-4.18.1-3.fc39.x86_64
libverto-0.3.2-5.fc38.x86_64
fedora-release-39-0.11.noarch
elfutils-default-yama-scope-0.189-2.fc39.noarch
gpg-pubkey-18b8e74c-62f2920f
popt-1.19-2.fc38.x86_64
libeconf-0.4.0-5.fc38.x86_64
libgomp-13.1.1-2.fc39.x86_64
openssl-libs-3.0.8-2.fc39.x86_64
rpm-sequoia-1.4.0-2.fc39.x86_64
bzip2-1.0.8-13.fc38.x86_64
glibc-2.37.9000-9.fc39.x86_64
crypto-policies-20230420-1.git3d08ae7.fc39.noarch
binutils-gold-2.40-7.fc39.x86_64
sed-4.8-12.fc38.x86_64
ansible-srpm-macros-1-10.fc39.noarch
pkgconf-pkg-config-1.9.4-2.fc39.x86_64
rpmautospec-rpm-macros-0.3.5-1.fc38.noarch
libmount-2.39-0.5.fc39.x86_64
util-linux-core-2.39-0.5.fc39.x86_64
publicsuffix-list-dafsa-20230318-1.fc39.noarch
Start: buildsrpm
Start: rpmbuild -bs
error: %changelog not in descending chronological order
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1684195200
Wrote: /builddir/build/SRPMS/mafft-7.520-1.20230516222539466786.mafft.fc39.src.rpm
Finish: rpmbuild -bs
cp: ‘var/lib/mock/fedora-rawhide-x86_64-1684275986.169171/root/var/log’: No such file or directory
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1684275986.169171/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-x86_64-1684275986.169171/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-x86_64-1684275986.169171/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-12e58v47/mafft/mafft.spec) Config(child) 1 minutes 36 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 (timeout=18000): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/mafft-7.520-1.20230516222539466786.mafft.fc39.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1684275986.169171 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)...
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/results/mafft-7.520-1.20230516222539466786.mafft.fc39.src.rpm)  Config(fedora-rawhide-x86_64)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1684275986.169171/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1684275986.169171/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: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1684275986.169171/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
Mock Version: 3.5
INFO: Mock Version: 3.5
Start: dnf update
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  28 kB/s | 1.5 kB     00:00    
fedora                                          147 kB/s | 5.8 kB     00:00    
Dependencies resolved.
Nothing to do.
Complete!
Finish: dnf update
Finish: chroot init
Start: build phase for mafft-7.520-1.20230516222539466786.mafft.fc39.src.rpm
Start: build setup for mafft-7.520-1.20230516222539466786.mafft.fc39.src.rpm
error: %changelog not in descending chronological order
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1684195200
Wrote: /builddir/build/SRPMS/mafft-7.520-1.20230516222539466786.mafft.fc39.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  33 kB/s | 1.5 kB     00:00    
fedora                                          115 kB/s | 5.8 kB     00:00    
Dependencies resolved.
================================================================================
 Package                Arch       Version                     Repository  Size
================================================================================
Installing:
 gcc                    x86_64     13.1.1-2.fc39               fedora      34 M
 gcc-c++                x86_64     13.1.1-2.fc39               fedora      13 M
 make                   x86_64     1:4.4.1-1.fc39              fedora     589 k
 zlib-devel             x86_64     1.2.13-3.fc38               fedora      45 k
Installing dependencies:
 annobin-docs           noarch     12.10-1.fc39                fedora      95 k
 annobin-plugin-gcc     x86_64     12.10-1.fc39                fedora     893 k
 cpp                    x86_64     13.1.1-2.fc39               fedora      11 M
 gc                     x86_64     8.2.2-3.fc38                fedora     110 k
 gcc-plugin-annobin     x86_64     13.1.1-2.fc39               fedora      44 k
 glibc-devel            x86_64     2.37.9000-9.fc39            fedora      69 k
 glibc-headers-x86      noarch     2.37.9000-9.fc39            fedora     549 k
 guile22                x86_64     2.2.7-8.fc39                fedora     6.5 M
 kernel-headers         x86_64     6.4.0-0.rc2.git0.1.fc39     fedora     1.5 M
 libmpc                 x86_64     1.3.1-2.fc38                fedora      70 k
 libstdc++-devel        x86_64     13.1.1-2.fc39               fedora     2.6 M
 libtool-ltdl           x86_64     2.4.7-6.fc38                fedora      37 k
 libunistring           x86_64     1.1-3.fc38                  fedora     545 k
 libxcrypt-devel        x86_64     4.4.33-7.fc39               fedora      30 k

Transaction Summary
================================================================================
Install  18 Packages

Total download size: 71 M
Installed size: 228 M
Downloading Packages:
(1/18): annobin-docs-12.10-1.fc39.noarch.rpm    1.1 MB/s |  95 kB     00:00    
(2/18): gc-8.2.2-3.fc38.x86_64.rpm              2.0 MB/s | 110 kB     00:00    
(3/18): annobin-plugin-gcc-12.10-1.fc39.x86_64. 6.3 MB/s | 893 kB     00:00    
(4/18): cpp-13.1.1-2.fc39.x86_64.rpm             21 MB/s |  11 MB     00:00    
(5/18): gcc-plugin-annobin-13.1.1-2.fc39.x86_64 2.5 MB/s |  44 kB     00:00    
(6/18): glibc-devel-2.37.9000-9.fc39.x86_64.rpm 3.9 MB/s |  69 kB     00:00    
(7/18): glibc-headers-x86-2.37.9000-9.fc39.noar 7.9 MB/s | 549 kB     00:00    
(8/18): gcc-c++-13.1.1-2.fc39.x86_64.rpm         24 MB/s |  13 MB     00:00    
(9/18): kernel-headers-6.4.0-0.rc2.git0.1.fc39.  13 MB/s | 1.5 MB     00:00    
(10/18): guile22-2.2.7-8.fc39.x86_64.rpm         31 MB/s | 6.5 MB     00:00    
(11/18): libmpc-1.3.1-2.fc38.x86_64.rpm         1.6 MB/s |  70 kB     00:00    
(12/18): libtool-ltdl-2.4.7-6.fc38.x86_64.rpm   978 kB/s |  37 kB     00:00    
(13/18): libunistring-1.1-3.fc38.x86_64.rpm      19 MB/s | 545 kB     00:00    
(14/18): libstdc++-devel-13.1.1-2.fc39.x86_64.r  29 MB/s | 2.6 MB     00:00    
(15/18): libxcrypt-devel-4.4.33-7.fc39.x86_64.r 1.4 MB/s |  30 kB     00:00    
(16/18): make-4.4.1-1.fc39.x86_64.rpm            13 MB/s | 589 kB     00:00    
(17/18): zlib-devel-1.2.13-3.fc38.x86_64.rpm    984 kB/s |  45 kB     00:00    
(18/18): gcc-13.1.1-2.fc39.x86_64.rpm            29 MB/s |  34 MB     00:01    
--------------------------------------------------------------------------------
Total                                            51 MB/s |  71 MB     00:01     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
  Installing       : libmpc-1.3.1-2.fc38.x86_64                            1/18 
  Installing       : cpp-13.1.1-2.fc39.x86_64                              2/18 
  Installing       : libunistring-1.1-3.fc38.x86_64                        3/18 
  Installing       : libtool-ltdl-2.4.7-6.fc38.x86_64                      4/18 
  Installing       : libstdc++-devel-13.1.1-2.fc39.x86_64                  5/18 
  Installing       : kernel-headers-6.4.0-0.rc2.git0.1.fc39.x86_64         6/18 
  Installing       : glibc-headers-x86-2.37.9000-9.fc39.noarch             7/18 
  Installing       : libxcrypt-devel-4.4.33-7.fc39.x86_64                  8/18 
  Installing       : glibc-devel-2.37.9000-9.fc39.x86_64                   9/18 
  Installing       : gc-8.2.2-3.fc38.x86_64                               10/18 
  Installing       : guile22-2.2.7-8.fc39.x86_64                          11/18 
  Installing       : make-1:4.4.1-1.fc39.x86_64                           12/18 
  Installing       : gcc-13.1.1-2.fc39.x86_64                             13/18 
  Running scriptlet: gcc-13.1.1-2.fc39.x86_64                             13/18 
  Installing       : annobin-docs-12.10-1.fc39.noarch                     14/18 
  Installing       : annobin-plugin-gcc-12.10-1.fc39.x86_64               15/18 
  Running scriptlet: annobin-plugin-gcc-12.10-1.fc39.x86_64               15/18 
  Installing       : gcc-c++-13.1.1-2.fc39.x86_64                         16/18 
  Installing       : gcc-plugin-annobin-13.1.1-2.fc39.x86_64              17/18 
  Running scriptlet: gcc-plugin-annobin-13.1.1-2.fc39.x86_64              17/18 
  Installing       : zlib-devel-1.2.13-3.fc38.x86_64                      18/18 
  Running scriptlet: zlib-devel-1.2.13-3.fc38.x86_64                      18/18 
  Verifying        : annobin-docs-12.10-1.fc39.noarch                      1/18 
  Verifying        : annobin-plugin-gcc-12.10-1.fc39.x86_64                2/18 
  Verifying        : cpp-13.1.1-2.fc39.x86_64                              3/18 
  Verifying        : gc-8.2.2-3.fc38.x86_64                                4/18 
  Verifying        : gcc-13.1.1-2.fc39.x86_64                              5/18 
  Verifying        : gcc-c++-13.1.1-2.fc39.x86_64                          6/18 
  Verifying        : gcc-plugin-annobin-13.1.1-2.fc39.x86_64               7/18 
  Verifying        : glibc-devel-2.37.9000-9.fc39.x86_64                   8/18 
  Verifying        : glibc-headers-x86-2.37.9000-9.fc39.noarch             9/18 
  Verifying        : guile22-2.2.7-8.fc39.x86_64                          10/18 
  Verifying        : kernel-headers-6.4.0-0.rc2.git0.1.fc39.x86_64        11/18 
  Verifying        : libmpc-1.3.1-2.fc38.x86_64                           12/18 
  Verifying        : libstdc++-devel-13.1.1-2.fc39.x86_64                 13/18 
  Verifying        : libtool-ltdl-2.4.7-6.fc38.x86_64                     14/18 
  Verifying        : libunistring-1.1-3.fc38.x86_64                       15/18 
  Verifying        : libxcrypt-devel-4.4.33-7.fc39.x86_64                 16/18 
  Verifying        : make-1:4.4.1-1.fc39.x86_64                           17/18 
  Verifying        : zlib-devel-1.2.13-3.fc38.x86_64                      18/18 

Installed:
  annobin-docs-12.10-1.fc39.noarch                                              
  annobin-plugin-gcc-12.10-1.fc39.x86_64                                        
  cpp-13.1.1-2.fc39.x86_64                                                      
  gc-8.2.2-3.fc38.x86_64                                                        
  gcc-13.1.1-2.fc39.x86_64                                                      
  gcc-c++-13.1.1-2.fc39.x86_64                                                  
  gcc-plugin-annobin-13.1.1-2.fc39.x86_64                                       
  glibc-devel-2.37.9000-9.fc39.x86_64                                           
  glibc-headers-x86-2.37.9000-9.fc39.noarch                                     
  guile22-2.2.7-8.fc39.x86_64                                                   
  kernel-headers-6.4.0-0.rc2.git0.1.fc39.x86_64                                 
  libmpc-1.3.1-2.fc38.x86_64                                                    
  libstdc++-devel-13.1.1-2.fc39.x86_64                                          
  libtool-ltdl-2.4.7-6.fc38.x86_64                                              
  libunistring-1.1-3.fc38.x86_64                                                
  libxcrypt-devel-4.4.33-7.fc39.x86_64                                          
  make-1:4.4.1-1.fc39.x86_64                                                    
  zlib-devel-1.2.13-3.fc38.x86_64                                               

Complete!
Finish: build setup for mafft-7.520-1.20230516222539466786.mafft.fc39.src.rpm
Start: rpmbuild mafft-7.520-1.20230516222539466786.mafft.fc39.src.rpm
error: %changelog not in descending chronological order
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1684195200
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.vZyJoL
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf mafft-v7.520
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/mafft-7.520.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd mafft-v7.520
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.8p964c
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd mafft-v7.520
+ cd core
+ make clean
rm -f *.o *.a *.exe *~ mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  mafft mafft-homologs.rb mafft-sparsecore.rb libdisttbfast.so libdisttbfast.dylib libdisttbfast.dll *.gcda *.gcno 
+ make 'CFLAGS=-fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
cp mafftash_premafft.tmpl mafftash_premafft.pl
cp seekquencer_premafft.tmpl seekquencer_premafft.pl
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c mtxutl.c
mtxutl.c: In function 'FreeFloatHalfMtx':
mtxutl.c:207:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  207 |                 if( mtx[i] ) FreeFloatVec( mtx[i] ); mtx[i] = NULL;
      |                 ^~
mtxutl.c:207:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  207 |                 if( mtx[i] ) FreeFloatVec( mtx[i] ); mtx[i] = NULL;
      |                                                      ^~~
mtxutl.c: In function 'FreeFloatMtx':
mtxutl.c:217:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  217 |                 if( mtx[i] ) FreeFloatVec( mtx[i] ); mtx[i] = NULL;
      |                 ^~
mtxutl.c:217:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  217 |                 if( mtx[i] ) FreeFloatVec( mtx[i] ); mtx[i] = NULL;
      |                                                      ^~~
mtxutl.c: In function 'FreeIntMtx':
mtxutl.c:396:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  396 |                 if( mtx[i] ) free( (char *)mtx[i] ); mtx[i] = NULL;
      |                 ^~
mtxutl.c:396:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  396 |                 if( mtx[i] ) free( (char *)mtx[i] ); mtx[i] = NULL;
      |                                                      ^~~
mtxutl.c: In function 'FreeIntCub':
mtxutl.c:460:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  460 |                 if( cub[i] ) FreeIntMtx( cub[i] ); cub[i] = NULL;
      |                 ^~
mtxutl.c:460:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  460 |                 if( cub[i] ) FreeIntMtx( cub[i] ); cub[i] = NULL;
      |                                                    ^~~
mtxutl.c: In function 'FreeDoubleHalfMtx':
mtxutl.c:515:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  515 |                 if( mtx[i] ) FreeFloatVec( mtx[i] ); mtx[i] = NULL;
      |                 ^~
mtxutl.c:515:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  515 |                 if( mtx[i] ) FreeFloatVec( mtx[i] ); mtx[i] = NULL;
      |                                                      ^~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c io.c
io.c: In function 'putlocalhom_str':
io.c:677:13: warning: variable 'sumoverlap' set but not used [-Wunused-but-set-variable]
  677 |         int sumoverlap;
      |             ^~~~~~~~~~
io.c:676:13: warning: variable 'isumscore' set but not used [-Wunused-but-set-variable]
  676 |         int isumscore;
      |             ^~~~~~~~~
io.c: In function 'Read':
io.c:1155:42: warning: argument 2 of type 'char[500000][256]' with mismatched bound [-Warray-parameter=]
 1155 |         extern void FRead( FILE *x, char y[M][B], int z[M], char **w );
      |                                     ~~~~~^~~~~~~
In file included from mltaln.h:344,
                 from io.c:1:
functions.h:201:35: note: previously declared as 'char[][256]'
  201 | extern void FRead( FILE *fp, char name[][B], int nlen[], char **seq );
      |                              ~~~~~^~~~~~~~~
io.c:1155:55: warning: argument 3 of type 'int[500000]' with mismatched bound [-Warray-parameter=]
 1155 |         extern void FRead( FILE *x, char y[M][B], int z[M], char **w );
      |                                                   ~~~~^~~~
functions.h:201:50: note: previously declared as 'int[]'
  201 | extern void FRead( FILE *fp, char name[][B], int nlen[], char **seq );
      |                                              ~~~~^~~~~~
io.c: In function 'ReadBlastm7_avscore':
io.c:3173:13: warning: variable 'nlocalhom' set but not used [-Wunused-but-set-variable]
 3173 |         int nlocalhom;
      |             ^~~~~~~~~
io.c:3170:35: warning: variable 'tend' set but not used [-Wunused-but-set-variable]
 3170 |         int qstart, qend, tstart, tend;
      |                                   ^~~~
io.c:3170:27: warning: variable 'tstart' set but not used [-Wunused-but-set-variable]
 3170 |         int qstart, qend, tstart, tend;
      |                           ^~~~~~
io.c:3170:21: warning: variable 'qend' set but not used [-Wunused-but-set-variable]
 3170 |         int qstart, qend, tstart, tend;
      |                     ^~~~
io.c:3170:13: warning: variable 'qstart' set but not used [-Wunused-but-set-variable]
 3170 |         int qstart, qend, tstart, tend;
      |             ^~~~~~
io.c: In function 'ReadBlastm7_scoreonly':
io.c:3299:13: warning: variable 'nlocalhom' set but not used [-Wunused-but-set-variable]
 3299 |         int nlocalhom;
      |             ^~~~~~~~~
io.c:3297:35: warning: variable 'tend' set but not used [-Wunused-but-set-variable]
 3297 |         int qstart, qend, tstart, tend;
      |                                   ^~~~
io.c:3297:27: warning: variable 'tstart' set but not used [-Wunused-but-set-variable]
 3297 |         int qstart, qend, tstart, tend;
      |                           ^~~~~~
io.c:3297:21: warning: variable 'qend' set but not used [-Wunused-but-set-variable]
 3297 |         int qstart, qend, tstart, tend;
      |                     ^~~~
io.c:3297:13: warning: variable 'qstart' set but not used [-Wunused-but-set-variable]
 3297 |         int qstart, qend, tstart, tend;
      |             ^~~~~~
io.c:3295:13: warning: variable 'overlapaa' set but not used [-Wunused-but-set-variable]
 3295 |         int overlapaa;
      |             ^~~~~~~~~
io.c: In function 'ReadBlastm7':
io.c:3414:35: warning: variable 'tend' set but not used [-Wunused-but-set-variable]
 3414 |         int qstart, qend, tstart, tend;
      |                                   ^~~~
io.c:3414:21: warning: variable 'qend' set but not used [-Wunused-but-set-variable]
 3414 |         int qstart, qend, tstart, tend;
      |                     ^~~~
io.c: In function 'codon2id':
io.c:6427:28: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
 6427 |         if( id0 < 0 || id1 < 0 | id2 < 0 ) return( -1 );
      |                        ~~~~^~~
io.c:6422:28: warning: unused variable 'id' [-Wunused-variable]
 6422 |         int id0, id1, id2, id;
      |                            ^~
io.c: In function 'PreRead':
io.c:1120:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1120 |         fgets( b, B-1, fp ); *locnjob = atoi( b );
      |         ^~~~~~~~~~~~~~~~~~~
io.c:1125:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1125 |                 fgets( b, B-1, fp );
      |                 ^~~~~~~~~~~~~~~~~~~
io.c:1129:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1129 |                         fgets( b, B-1, fp ); nleni = atoi( b );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'FRead':
io.c:1165:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1165 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c:1255:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1255 |                 fgets( b, B-1, fp ); nlen[i] = atoi( b );      /* seq i no nagasa */
      |                 ^~~~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_doublehalf_part_pointer':
io.c:2708:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2708 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2710:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2710 |     fgets( b, B, fp ); nseq0 = atoi( b );  // 2020/Oct/23
      |     ^~~~~~~~~~~~~~~~~
io.c:2716:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2716 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_doublehalf_pointer':
io.c:2746:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2746 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2747:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2747 |     fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 )
      |     ^~~~~~~~~~~~~~~~~
io.c:2752:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2752 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_doublehalf':
io.c:2780:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2780 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2781:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2781 |     fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
      |     ^~~~~~~~~~~~~~~~~
io.c:2782:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2782 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_double':
io.c:2810:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2810 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2811:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2811 |     fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
      |     ^~~~~~~~~~~~~~~~~
io.c:2812:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2812 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_int':
io.c:2840:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2840 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2841:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2841 |     fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
      |     ^~~~~~~~~~~~~~~~~
io.c:2842:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2842 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2_pointer':
io.c:2871:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2871 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2872:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2872 |     fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
      |     ^~~~~~~~~~~~~~~~~
io.c:2873:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2873 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'readhat2':
io.c:2901:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2901 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c:2902:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2902 |     fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." );
      |     ^~~~~~~~~~~~~~~~~
io.c:2903:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2903 |     fgets( b, B, fp );
      |     ^~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta_sub':
io.c:3103:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3103 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c:3118:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3118 |             fgets( b, B-1, fp );
      |             ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadSsearch':
io.c:3137:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3137 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadBlastm7_avscore':
io.c:3265:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3265 |                 fgets( b, B-1, fp );
      |                 ^~~~~~~~~~~~~~~~~~~
io.c:3272:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3272 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c:3273:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3273 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadBlastm7_scoreonly':
io.c:3388:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3388 |                 fgets( b, B-1, fp );
      |                 ^~~~~~~~~~~~~~~~~~~
io.c:3395:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3395 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c:3396:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3396 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadBlastm7':
io.c:3506:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3506 |                 fgets( b, B-1, fp );
      |                 ^~~~~~~~~~~~~~~~~~~
io.c:3513:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3513 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c:3514:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3514 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34noalign':
io.c:3538:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3538 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10_nuc':
io.c:3575:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3575 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c:3601:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3601 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10':
io.c:3714:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3714 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c:3738:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3738 |                         fgets( b, B-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10_scoreonly_nucbk':
io.c:3841:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3841 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10_scoreonly_nuc':
io.c:3891:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3891 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34m10_scoreonly':
io.c:3952:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 3952 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta34':
io.c:4008:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4008 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c:4034:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4034 |                 fgets( b, B-1, fp ); // initn:
      |                 ^~~~~~~~~~~~~~~~~~~
io.c:4037:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4037 |                 fgets( b, B-1, fp ); // Smith-Waterman score
      |                 ^~~~~~~~~~~~~~~~~~~
io.c:4049:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4049 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta3':
io.c:4071:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4071 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadFasta':
io.c:4096:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4096 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadOpt':
io.c:4133:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4133 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'ReadOpt2':
io.c:4154:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4154 |         fgets( b, B-1, fp );
      |         ^~~~~~~~~~~~~~~~~~~
io.c: In function 'readOtherOptions':
io.c:4250:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 4250 |                 fgets( b, B-1, fp );
      |                 ^~~~~~~~~~~~~~~~~~~
io.c: In function 'loadaamtx':
io.c:5509:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5509 |                 fgets( inorder, 999, mf );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~
io.c:5541:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5541 |                 fgets( line, 999, mf );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c:5564:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5564 |                 fgets( line, 999, mf );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'readsubalignmentstable':
io.c:5720:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5720 |                         fgets( line, linelen-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
io.c:5741:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5741 |                         fgets( line, linelen-1, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'readmccaskill':
io.c:5795:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5795 |         fgets( gett, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~
io.c:5805:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5805 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'readpairfoldalign':
io.c:5864:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5864 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c:5877:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5877 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c:5884:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5884 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c:5898:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5898 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c:5904:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 5904 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
io.c: In function 'readexternalanchors':
io.c:6342:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 6342 |                 fgets( buf, 9999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c mltaln9.c
mltaln9.c: In function 'score_calc5':
mltaln9.c:482:12: warning: variable 'c' set but not used [-Wunused-but-set-variable]
  482 |     double c;
      |            ^
mltaln9.c: In function 'setnearest_double_fullmtx':
mltaln9.c:1447:18: warning: variable 'effptpt' set but not used [-Wunused-but-set-variable]
 1447 |         double **effptpt;
      |                  ^~~~~~~
mltaln9.c: In function 'loadtree':
mltaln9.c:2494:46: warning: variable 'maxijm' set but not used [-Wunused-but-set-variable]
 2494 |         int i, j, k, miniim, maxiim, minijm, maxijm;
      |                                              ^~~~~~
mltaln9.c:2494:38: warning: variable 'minijm' set but not used [-Wunused-but-set-variable]
 2494 |         int i, j, k, miniim, maxiim, minijm, maxijm;
      |                                      ^~~~~~
mltaln9.c:2494:30: warning: variable 'maxiim' set but not used [-Wunused-but-set-variable]
 2494 |         int i, j, k, miniim, maxiim, minijm, maxijm;
      |                              ^~~~~~
mltaln9.c:2494:22: warning: variable 'miniim' set but not used [-Wunused-but-set-variable]
 2494 |         int i, j, k, miniim, maxiim, minijm, maxijm;
      |                      ^~~~~~
mltaln9.c: In function 'msaresetnearestthread':
mltaln9.c:3630:17: warning: variable 'acptinit' set but not used [-Wunused-but-set-variable]
 3630 |         Bchain *acptinit;
      |                 ^~~~~~~~
mltaln9.c: In function 'kmerresetnearestthread':
mltaln9.c:3721:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3721 |                                 if( pointt ) free( singlettable1 ); singlettable1 = NULL;// kmer
      |                                 ^~
mltaln9.c:3721:69: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3721 |                                 if( pointt ) free( singlettable1 ); singlettable1 = NULL;// kmer
      |                                                                     ^~~~~~~~~~~~~
mltaln9.c:3686:17: warning: variable 'acptinit' set but not used [-Wunused-but-set-variable]
 3686 |         Bchain *acptinit;
      |                 ^~~~~~~~
mltaln9.c: In function 'compacttree_memsaveselectable':
mltaln9.c:5941:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5941 |                 if( partmtx[im] ) free( partmtx[im] ); partmtx[im] = NULL;
      |                 ^~
mltaln9.c:5941:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5941 |                 if( partmtx[im] ) free( partmtx[im] ); partmtx[im] = NULL;
      |                                                        ^~~~~~~
mltaln9.c:5942:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5942 |                 if( partmtx[jm] ) free( partmtx[jm] ); partmtx[jm] = NULL;
      |                 ^~
mltaln9.c:5942:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5942 |                 if( partmtx[jm] ) free( partmtx[jm] ); partmtx[jm] = NULL;
      |                                                        ^~~~~~~
mltaln9.c:6108:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 6108 |                 if( partmtx[im] ) free( partmtx[im] ); partmtx[im] = NULL;
      |                 ^~
mltaln9.c:6108:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 6108 |                 if( partmtx[im] ) free( partmtx[im] ); partmtx[im] = NULL;
      |                                                        ^~~~~~~
mltaln9.c:5513:18: warning: variable 'clusterfuncpt' set but not used [-Wunused-but-set-variable]
 5513 |         double (*clusterfuncpt[1])(double,double);
      |                  ^~~~~~~~~~~~~
mltaln9.c: In function 'DSPscore':
mltaln9.c:11228:12: warning: variable 'c' set but not used [-Wunused-but-set-variable]
11228 |     double c;
      |            ^
mltaln9.c: In function 'searchAnchors':
mltaln9.c:11291:13: warning: unused variable 'alloclen' [-Wunused-variable]
11291 |         int alloclen = 0;
      |             ^~~~~~~~
mltaln9.c: In function 'new_OpeningGapCount':
mltaln9.c:12599:41: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12599 |                                 if( !gb *  gc ) *fpt += feff;
      |                                     ~~~~^~~~~
mltaln9.c: In function 'new_OpeningGapCount_zure':
mltaln9.c:12653:41: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12653 |                                 if( !gb *  gc ) *fpt += feff;
      |                                     ~~~~^~~~~
mltaln9.c:12660:33: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12660 |                         if( !gb *  gc ) *fpt += feff;
      |                             ~~~~^~~~~
mltaln9.c: In function 'new_FinalGapCount_zure':
mltaln9.c:12716:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12716 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c:12724:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12724 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c: In function 'new_FinalGapCount':
mltaln9.c:12780:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12780 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c:12788:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12788 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c: In function 'st_OpeningGapAdd':
mltaln9.c:12822:33: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12822 |                         if( !gb *  gc ) *fpt += feff;
      |                             ~~~~^~~~~
mltaln9.c: In function 'st_OpeningGapCount':
mltaln9.c:12860:41: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12860 |                                 if( !gb *  gc ) *fpt += feff;
      |                                     ~~~~^~~~~
mltaln9.c: In function 'st_FinalGapCount_zure':
mltaln9.c:12891:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12891 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c:12900:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12900 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c: In function 'st_FinalGapAdd':
mltaln9.c:12935:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12935 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c:12945:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12945 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c: In function 'st_FinalGapCount':
mltaln9.c:12974:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12974 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c:12983:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
12983 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c: In function 'getGapPattern':
mltaln9.c:13011:40: warning: '*' in boolean context, suggest '&&' instead [-Wint-in-bool-context]
13011 |                                 if( gb * !gc ) *fpt += feff;
      |                                     ~~~^~~~~
mltaln9.c: In function 'addonetip2fixedpos':
mltaln9.c:13954:13: warning: variable 'seqlengthcondition' set but not used [-Wunused-but-set-variable]
13954 |         int seqlengthcondition;
      |             ^~~~~~~~~~~~~~~~~~
mltaln9.c: In function 'makeskiptable':
mltaln9.c:15247:29: warning: variable 'gaplen' set but not used [-Wunused-but-set-variable]
15247 |         int i, j, posinseq, gaplen;
      |                             ^~~~~~
mltaln9.c: In function 'readlocalhomfromfile_autofid':
mltaln9.c:15740:17: warning: variable 'k2' set but not used [-Wunused-but-set-variable]
15740 |         int k1, k2;
      |                 ^~
mltaln9.c:15740:13: warning: variable 'k1' set but not used [-Wunused-but-set-variable]
15740 |         int k1, k2;
      |             ^~
mltaln9.c: In function 'check_guidetreefile':
mltaln9.c:2850:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 2850 |         fgets( string, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c: In function 'readlocalhomtable2_single_bin_noseek':
mltaln9.c:15688:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
15688 |         fread( &size, sizeof( int ), 1, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:15689:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
15689 |         fread( &opt, sizeof( double ), 1, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:15692:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
15692 |         fread( m, size*sizeof( int ), 3, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:15728:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
15728 |         fread( &c, sizeof( char ), 1, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c: At top level:
mltaln9.c:1852:12: warning: 'compfuncpair' defined but not used [-Wunused-function]
 1852 | static int compfuncpair( const void *p, const void *q )
      |            ^~~~~~~~~~~~
mltaln9.c: In function 'calcnearestthread':
mltaln9.c:4557:35: warning: 'distfunc' may be used uninitialized [-Wmaybe-uninitialized]
 4557 |                         tmpdist = distfunc( bseq[pos], bseq[i], selfscore[pos], selfscore[i], alloclen );
      |                                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:4500:18: note: 'distfunc' was declared here
 4500 |         double (*distfunc)( char *, char *, double, double, int );
      |                  ^~~~~~~~
mltaln9.c:4566:32: warning: 'neighbor' may be used uninitialized [-Wmaybe-uninitialized]
 4566 |                 neighbors[pos] = neighbor;
      |                 ~~~~~~~~~~~~~~~^~~~~~~~~~
mltaln9.c:4499:13: note: 'neighbor' was declared here
 4499 |         int neighbor, i;
      |             ^~~~~~~~
mltaln9.c: In function 'createchain':
mltaln9.c:2161:75: warning: 'tree' may be used uninitialized [-Wmaybe-uninitialized]
 2161 |                 posinit += sprintf( instanttree+posinit, "%s:%7.5f,", tree[im], len[0][0] );
      |                                                                           ^
mltaln9.c:2063:16: note: 'tree' was declared here
 2063 |         char **tree;
      |                ^~~~
mltaln9.c:2161:28: warning: 'instanttree' may be used uninitialized [-Wmaybe-uninitialized]
 2161 |                 posinit += sprintf( instanttree+posinit, "%s:%7.5f,", tree[im], len[0][0] );
      |                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:2064:15: note: 'instanttree' was declared here
 2064 |         char *instanttree;
      |               ^~~~~~~~~~~
mltaln9.c:2161:25: warning: 'posinit' may be used uninitialized [-Wmaybe-uninitialized]
 2161 |                 posinit += sprintf( instanttree+posinit, "%s:%7.5f,", tree[im], len[0][0] );
      |                         ^~
mltaln9.c:2065:13: note: 'posinit' was declared here
 2065 |         int posinit;
      |             ^~~~~~~
mltaln9.c:2281:17: warning: 'nametmp' may be used uninitialized [-Wmaybe-uninitialized]
 2281 |                 free( nametmp );
      |                 ^~~~~~~~~~~~~~~
mltaln9.c:2067:15: note: 'nametmp' was declared here
 2067 |         char *nametmp, *nameptr, *tmpptr;
      |               ^~~~~~~
mltaln9.c:2113:31: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 2113 |                 instanttree = calloc( treelen, sizeof( char ) );
      |                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from mltaln.h:13,
                 from mltaln9.c:1:
/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
mltaln9.c:2124:17: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 2124 |         order = calloc( nseq, sizeof( int ) );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
mltaln9.c: In function 'loadtree':
mltaln9.c:2751:86: warning: 'tree' may be used uninitialized [-Wmaybe-uninitialized]
 2751 |                         treetmp = realloc( treetmp, strlen( tree[im] ) + strlen( tree[jm] ) + 100 ); // 22 de juubunn (:%7,:%7) %7 ha minus kamo
      |                                                                                      ^
mltaln9.c:2505:16: note: 'tree' was declared here
 2505 |         char **tree;
      |                ^~~~
mltaln9.c:2822:17: warning: 'nametmp' may be used uninitialized [-Wmaybe-uninitialized]
 2822 |                 free( nametmp );
      |                 ^~~~~~~~~~~~~~~
mltaln9.c:2507:15: note: 'nametmp' was declared here
 2507 |         char *nametmp, *nameptr, *tmpptr;
      |               ^~~~~~~
In file included from /usr/include/stdio.h:964,
                 from mltaln.h:12:
In function 'fgets',
    inlined from 'check_guidetreefile' at mltaln9.c:2850:2:
/usr/include/bits/stdio2.h:215:12: warning: call to '*__fgets_chk' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  215 |     return __fgets_chk_warn (__s, sz, __n, __stream);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'includemember',
    inlined from 'recalcpairs_para4' at mltaln9.c:5020:9,
    inlined from 'compacttreedpdist' at mltaln9.c:5469:2:
mltaln9.c:15069:31: warning: 'addmem' may be used uninitialized [-Wmaybe-uninitialized]
15069 |                 for( j=0; cand[j]>-1; j++ )
      |                           ~~~~^~~
mltaln9.c: In function 'compacttreedpdist':
mltaln9.c:4913:39: note: 'addmem' was declared here
 4913 |         int **memhist, *mem0, *mem1, *addmem;
      |                                       ^~~~~~
mltaln9.c: In function 'compacttree_memsaveselectable':
mltaln9.c:5964:86: warning: 'tree' may be used uninitialized [-Wmaybe-uninitialized]
 5964 |                         treetmp = realloc( treetmp, strlen( tree[im] ) + strlen( tree[jm] ) + 100 ); // 22 de juubunn (:%7,:%7) %7 ha minus kamo
      |                                                                                      ^
mltaln9.c:5509:16: note: 'tree' was declared here
 5509 |         char **tree; //static?
      |                ^~~~
mltaln9.c:6116:17: warning: 'nametmp' may be used uninitialized [-Wmaybe-uninitialized]
 6116 |                 free( nametmp );
      |                 ^~~~~~~~~~~~~~~
mltaln9.c:5511:15: note: 'nametmp' was declared here
 5511 |         char *nametmp, *nameptr, *tmpptr; //static?
      |               ^~~~~~~
mltaln9.c: In function 'fixed_musclesupg_double_realloc_nobk_halfmtx_treeout_memsave':
mltaln9.c:6531:28: warning: 'density' may be used uninitialized [-Wmaybe-uninitialized]
 6531 |         if( treeout == 2 ) free( density );
      |                            ^~~~~~~~~~~~~~~
mltaln9.c:6156:17: note: 'density' was declared here
 6156 |         double *density;
      |                 ^~~~~~~
mltaln9.c:6494:28: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 6494 |                 int *mem = calloc( sizeof( int ), nseq );
      |                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
mltaln9.c: In function 'fixed_supg_double_treeout_constrained':
mltaln9.c:7515:42: warning: 'testtopol' may be used uninitialized [-Wmaybe-uninitialized]
 7515 |                                 *intpt++ = im;
      |                                 ~~~~~~~~~^~~~
mltaln9.c:7283:14: note: 'testtopol' was declared here
 7283 |         int *testtopol, **inconsistent;
      |              ^~~~~~~~~
mltaln9.c:7438:67: warning: 'inconsistent' may be used uninitialized [-Wmaybe-uninitialized]
 7438 |                 for( i=0; i<ninconsistentpairs; i++ ) inconsistent[inconsistentpairlist[i][0]][inconsistentpairlist[i][1]] = 0;
      |                                                                   ^
mltaln9.c:7283:27: note: 'inconsistent' was declared here
 7283 |         int *testtopol, **inconsistent;
      |                           ^~~~~~~~~~~~
mltaln9.c:7551:60: warning: 'warned' may be used uninitialized [-Wmaybe-uninitialized]
 7551 |                                                 if( !warned[i] )
      |                                                            ^
mltaln9.c:7287:14: note: 'warned' was declared here
 7287 |         int *warned;
      |              ^~~~~~
mltaln9.c:7562:80: warning: 'inconsistentpairlist' may be used uninitialized [-Wmaybe-uninitialized]
 7562 |                                                         inconsistentpairlist = realloc( inconsistentpairlist, (ninconsistentpairs+1)*sizeof( int * ) );
      |                                                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mltaln9.c:7284:15: note: 'inconsistentpairlist' was declared here
 7284 |         int **inconsistentpairlist;
      |               ^~~~~~~~~~~~~~~~~~~~
mltaln9.c: In function 'addonetip2fixedpos':
mltaln9.c:14257:55: warning: 'addedlen' may be used uninitialized [-Wmaybe-uninitialized]
14257 |                         lenc[posinnew][0] = len[i][0] - addedlen; // 2014/6/10
      |                                             ~~~~~~~~~~^~~~~~~~~~
mltaln9.c:13939:49: note: 'addedlen' was declared here
13939 |         double minscore, minscoreo, eff0, eff1, addedlen, tmpmin;
      |                                                 ^~~~~~~~
mltaln9.c:14440:15: warning: 'neighbor' may be used uninitialized [-Wmaybe-uninitialized]
14440 |         return( neighbor );
      |               ^
mltaln9.c:13946:13: note: 'neighbor' was declared here
13946 |         int neighbor;
      |             ^~~~~~~~
mltaln9.c: In function 'addonetip':
mltaln9.c:14759:55: warning: 'addedlen' may be used uninitialized [-Wmaybe-uninitialized]
14759 |                         lenc[posinnew][0] = len[i][0] - addedlen; // 2014/6/10
      |                                             ~~~~~~~~~~^~~~~~~~~~
mltaln9.c:14448:49: note: 'addedlen' was declared here
14448 |         double minscore, minscoreo, eff0, eff1, addedlen, tmpmin;
      |                                                 ^~~~~~~~
mltaln9.c:14942:15: warning: 'neighbor' may be used uninitialized [-Wmaybe-uninitialized]
14942 |         return( neighbor );
      |               ^
mltaln9.c:14455:13: note: 'neighbor' was declared here
14455 |         int neighbor;
      |             ^~~~~~~~
mltaln9.c: In function 'fillimp_file':
mltaln9.c:16019:20: warning: 'handle' may be used uninitialized [-Wmaybe-uninitialized]
16019 |         pthread_t *handle;
      |                    ^~~~~~
mltaln9.c:16194:61: warning: 'localimpmtx' may be used uninitialized [-Wmaybe-uninitialized]
16194 |                                 targ[i].impmtx = localimpmtx[i];
      |                                                  ~~~~~~~~~~~^~~
mltaln9.c:16021:19: note: 'localimpmtx' was declared here
16021 |         double ***localimpmtx;
      |                   ^~~~~~~~~~~
mltaln9.c:16023:29: warning: 'localndone' may be used uninitialized [-Wmaybe-uninitialized]
16023 |         unsigned long long *localndone;
      |                             ^~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c tddis.c
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c constants.c
In file included from constants.c:6:
JTT.c:9:56: warning: argument 3 of type 'unsigned char[26]' with mismatched bound [-Warray-parameter=]
    9 | void JTTmtx( double **rsr, double *freq, unsigned char locamino[26], char locgrp[26], int isTM )
      |                                          ~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from mltaln.h:344,
                 from constants.c:1:
functions.h:181:63: note: previously declared as 'unsigned char[128]'
  181 | extern void JTTmtx( double **rsr, double *freq, unsigned char locamino[0x80], char locgrp[0x80], int isTM );
      |                                                 ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
JTT.c:9:75: warning: argument 4 of type 'char[26]' with mismatched bound [-Warray-parameter=]
    9 | void JTTmtx( double **rsr, double *freq, unsigned char locamino[26], char locgrp[26], int isTM )
      |                                                                      ~~~~~^~~~~~~~~~
functions.h:181:84: note: previously declared as 'char[128]'
  181 | extern void JTTmtx( double **rsr, double *freq, unsigned char locamino[0x80], char locgrp[0x80], int isTM );
      |                                                                               ~~~~~^~~~~~~~~~~~
In file included from constants.c:7:
blosum.c: In function 'extendedmtx':
blosum.c:429:30: warning: operation on '*(*(matrix + (sizetype)((long unsigned int)i * 8)) + (sizetype)((long unsigned int)i * 8))' may be undefined [-Wsequence-point]
  429 |                 matrix[i][i] = matrix[i][i] = (double)1.0;
      |                 ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
constants.c: In function 'constants':
constants.c:713:39: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
  713 |                 if( userdefined ) if( i=checkscoremtx( n_distmp, nseq, seq ) )
      |                                       ^
constants.c: In function 'freeconstants':
constants.c:1542:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1542 |         if( n_disLN ) FreeDoubleMtx( n_disLN ); n_disLN = NULL;
      |         ^~
constants.c:1542:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1542 |         if( n_disLN ) FreeDoubleMtx( n_disLN ); n_disLN = NULL;
      |                                                 ^~~~~~~
constants.c:1543:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1543 |         if( n_dis ) FreeIntMtx( n_dis ); n_dis = NULL;
      |         ^~
constants.c:1543:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1543 |         if( n_dis ) FreeIntMtx( n_dis ); n_dis = NULL;
      |                                          ^~~~~
constants.c:1544:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1544 |         if( n_disFFT ) FreeIntMtx( n_disFFT ); n_disFFT = NULL;
      |         ^~
constants.c:1544:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1544 |         if( n_disFFT ) FreeIntMtx( n_disFFT ); n_disFFT = NULL;
      |                                                ^~~~~~~~
constants.c:1545:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1545 |         if( n_dis_consweight_multi ) FreeDoubleMtx( n_dis_consweight_multi ); n_dis_consweight_multi = NULL;
      |         ^~
constants.c:1545:79: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1545 |         if( n_dis_consweight_multi ) FreeDoubleMtx( n_dis_consweight_multi ); n_dis_consweight_multi = NULL;
      |                                                                               ^~~~~~~~~~~~~~~~~~~~~~
constants.c:1546:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1546 |         if( amino_dis ) FreeIntMtx( amino_dis ); amino_dis = NULL;
      |         ^~
constants.c:1546:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1546 |         if( amino_dis ) FreeIntMtx( amino_dis ); amino_dis = NULL;
      |                                                  ^~~~~~~~~
constants.c:1547:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1547 |         if( amino_dis_consweight_multi ) FreeDoubleMtx( amino_dis_consweight_multi ); amino_dis_consweight_multi = NULL;
      |         ^~
constants.c:1547:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1547 |         if( amino_dis_consweight_multi ) FreeDoubleMtx( amino_dis_consweight_multi ); amino_dis_consweight_multi = NULL;
      |                                                                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~
blosum.c: In function 'overridematrix':
blosum.c:372:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  372 |                 fgets( buf, 499, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c nj.c
nj.c: In function 'nj':
nj.c:168:43: warning: 'r' may be used uninitialized [-Wmaybe-uninitialized]
  168 |     len2 = ( mtx[MIN(i,im)][MAX(i,im)] - r[im] + r[i] ) / 2;
      |                                          ~^~~~
nj.c:85:12: note: 'r' declared here
   85 |     double r[M];
      |            ^
nj.c:168:43: warning: 'r' may be used uninitialized [-Wmaybe-uninitialized]
  168 |     len2 = ( mtx[MIN(i,im)][MAX(i,im)] - r[im] + r[i] ) / 2;
      |                                          ~^~~~
nj.c:85:12: note: 'r' declared here
   85 |     double r[M];
      |            ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c partSalignmm.c  
partSalignmm.c: In function 'Atracking':
partSalignmm.c:542:59: warning: variable 'lastk' set but not used [-Wunused-but-set-variable]
  542 |         int i, j, l, iin, jin, ifi, jfi, lgth1, lgth2, k, lastk, limk;
      |                                                           ^~~~~
partSalignmm.c: In function 'partA__align_variousdist':
partSalignmm.c:1859:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1859 |                         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |                         ^~
partSalignmm.c:1859:80: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1859 |                         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |                                                                                ^~~~~~~~~
partSalignmm.c:1860:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1860 |                         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |                         ^~
partSalignmm.c:1860:80: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1860 |                         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |                                                                                ^~~~~~~~~
partSalignmm.c:1861:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 1861 |                         if( nmask ) free( nmask ); nmask = NULL;
      |                         ^~
partSalignmm.c:1861:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 1861 |                         if( nmask ) free( nmask ); nmask = NULL;
      |                                                    ^~~~~
partSalignmm.c:2114:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2114 |         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |         ^~
partSalignmm.c:2114:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2114 |         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |                                                                ^~~~~~~~~
partSalignmm.c:2115:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2115 |         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |         ^~
partSalignmm.c:2115:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2115 |         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |                                                                ^~~~~~~~~
partSalignmm.c:2116:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2116 |         if( nmask ) free( nmask ); nmask = NULL;
      |         ^~
partSalignmm.c:2116:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2116 |         if( nmask ) free( nmask ); nmask = NULL;
      |                                    ^~~~~
partSalignmm.c: In function 'partA__align':
partSalignmm.c:1268:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1268 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
partSalignmm.c:743:17: note: 'wmrecordspt' was declared here
  743 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
partSalignmm.c:1268:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 1268 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
partSalignmm.c:743:31: note: 'wmrecords1pt' was declared here
  743 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
partSalignmm.c:1248:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1248 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
partSalignmm.c:743:46: note: 'prevwmrecordspt' was declared here
  743 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
partSalignmm.c:1271:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 1271 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
partSalignmm.c:744:14: note: 'warpipt' was declared here
  744 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
partSalignmm.c:1272:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 1272 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
partSalignmm.c:744:24: note: 'warpjpt' was declared here
  744 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
partSalignmm.c: In function 'partA__align_variousdist':
partSalignmm.c:2012:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 2012 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
partSalignmm.c:1439:17: note: 'wmrecordspt' was declared here
 1439 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
partSalignmm.c:2012:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 2012 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
partSalignmm.c:1439:31: note: 'wmrecords1pt' was declared here
 1439 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
partSalignmm.c:1992:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1992 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
partSalignmm.c:1439:46: note: 'prevwmrecordspt' was declared here
 1439 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
partSalignmm.c:2015:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 2015 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
partSalignmm.c:1440:14: note: 'warpipt' was declared here
 1440 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
partSalignmm.c:2016:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 2016 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
partSalignmm.c:1440:24: note: 'warpjpt' was declared here
 1440 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Lalignmm.c 
Lalignmm.c: In function 'MSalign2m2m_rec':
Lalignmm.c:393:15: warning: variable 'gaps' set but not used [-Wunused-but-set-variable]
  393 |         char *gaps;
      |               ^~~~
Lalignmm.c: In function 'Lalignmm_hmout':
Lalignmm.c:2180:21: warning: variable 'nglen2' set but not used [-Wunused-but-set-variable]
 2180 |         int nglen1, nglen2;
      |                     ^~~~~~
Lalignmm.c:2180:13: warning: variable 'nglen1' set but not used [-Wunused-but-set-variable]
 2180 |         int nglen1, nglen2;
      |             ^~~~~~
Lalignmm.c: In function 'Lalign2m2m_hmout':
Lalignmm.c:2381:21: warning: variable 'nglen2' set but not used [-Wunused-but-set-variable]
 2381 |         int nglen1, nglen2;
      |                     ^~~~~~
Lalignmm.c:2381:13: warning: variable 'nglen1' set but not used [-Wunused-but-set-variable]
 2381 |         int nglen1, nglen2;
      |             ^~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c rna.c 
rna.c: In function 'rnaalifoldcall':
rna.c:225:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  225 |         system( cmd );
      |         ^~~~~~~~~~~~~
rna.c:245:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  245 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
rna.c:285:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  285 |         system( cmd );
      |         ^~~~~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Salignmm.c 
Salignmm.c: In function 'A__align_variousdist':
Salignmm.c:2811:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2811 |                         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |                         ^~
Salignmm.c:2811:80: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2811 |                         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |                                                                                ^~~~~~~~~
Salignmm.c:2812:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2812 |                         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |                         ^~
Salignmm.c:2812:80: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2812 |                         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |                                                                                ^~~~~~~~~
Salignmm.c:2813:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2813 |                         if( nmask ) free( nmask ); nmask = NULL;
      |                         ^~
Salignmm.c:2813:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2813 |                         if( nmask ) free( nmask ); nmask = NULL;
      |                                                    ^~~~~
Salignmm.c:3099:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3099 |         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |         ^~
Salignmm.c:3099:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3099 |         if( masklist1 ) freeintmtx( masklist1, maxdistclass ); masklist1 = NULL;
      |                                                                ^~~~~~~~~
Salignmm.c:3100:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3100 |         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |         ^~
Salignmm.c:3100:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3100 |         if( masklist2 ) freeintmtx( masklist2, maxdistclass ); masklist2 = NULL;
      |                                                                ^~~~~~~~~
Salignmm.c:3101:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3101 |         if( nmask ) free( nmask ); nmask = NULL;
      |         ^~
Salignmm.c:3101:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3101 |         if( nmask ) free( nmask ); nmask = NULL;
      |                                    ^~~~~
Salignmm.c: In function 'Atracking':
Salignmm.c:1083:15: warning: 'wm' may be used uninitialized [-Wmaybe-uninitialized]
 1083 |         return( wm );
      |               ^
Salignmm.c:860:16: note: 'wm' was declared here
  860 |         double wm;
      |                ^~
Salignmm.c: In function 'A__align':
Salignmm.c:1987:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1987 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Salignmm.c:1165:17: note: 'wmrecordspt' was declared here
 1165 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Salignmm.c:1987:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 1987 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Salignmm.c:1165:31: note: 'wmrecords1pt' was declared here
 1165 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Salignmm.c:1960:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1960 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Salignmm.c:1165:46: note: 'prevwmrecordspt' was declared here
 1165 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Salignmm.c:1990:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 1990 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Salignmm.c:1166:14: note: 'warpipt' was declared here
 1166 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Salignmm.c:1991:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 1991 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Salignmm.c:1166:24: note: 'warpjpt' was declared here
 1166 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
Salignmm.c: In function 'A__align_variousdist':
Salignmm.c:2990:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 2990 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Salignmm.c:2293:17: note: 'wmrecordspt' was declared here
 2293 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Salignmm.c:2990:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 2990 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Salignmm.c:2293:31: note: 'wmrecords1pt' was declared here
 2293 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Salignmm.c:2968:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 2968 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_shift + fpenalty_ex * ( i - prevwarpi[j-1] + j - prevwarpj[j-1] ) ) > wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Salignmm.c:2293:46: note: 'prevwmrecordspt' was declared here
 2293 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Salignmm.c:2993:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 2993 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Salignmm.c:2294:14: note: 'warpipt' was declared here
 2294 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Salignmm.c:2994:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 2994 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Salignmm.c:2294:24: note: 'warpjpt' was declared here
 2294 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Dalignmm.c 
Dalignmm.c: In function 'calcpfac_gapex_noidatend':
Dalignmm.c:1576:29: warning: variable 'pfac2' set but not used [-Wunused-but-set-variable]
 1576 |         double pfac, pfac1, pfac2, pfac10;
      |                             ^~~~~
Dalignmm.c: In function 'D__align':
Dalignmm.c:2640:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2640 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                         ^~
Dalignmm.c:2640:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2640 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2641:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2641 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                         ^~
Dalignmm.c:2641:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2641 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2642:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2642 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                         ^~
Dalignmm.c:2642:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2642 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2643:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2643 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                         ^~
Dalignmm.c:2643:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2643 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2645:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2645 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                         ^~
Dalignmm.c:2645:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2645 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2646:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2646 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                         ^~
Dalignmm.c:2646:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2646 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2647:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2647 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                         ^~
Dalignmm.c:2647:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2647 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2648:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2648 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                         ^~
Dalignmm.c:2648:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2648 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2649:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2649 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                         ^~
Dalignmm.c:2649:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2649 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2650:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2650 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                         ^~
Dalignmm.c:2650:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2650 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2651:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2651 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                         ^~
Dalignmm.c:2651:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2651 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2652:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2652 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                         ^~
Dalignmm.c:2652:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2652 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2653:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2653 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                         ^~
Dalignmm.c:2653:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2653 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:2654:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2654 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                         ^~
Dalignmm.c:2654:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2654 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:2778:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2778 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                         ^~
Dalignmm.c:2778:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2778 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2779:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2779 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                         ^~
Dalignmm.c:2779:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2779 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2780:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2780 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                         ^~
Dalignmm.c:2780:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2780 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2781:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2781 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                         ^~
Dalignmm.c:2781:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2781 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2783:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2783 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                         ^~
Dalignmm.c:2783:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2783 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2784:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2784 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                         ^~
Dalignmm.c:2784:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2784 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2785:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2785 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                         ^~
Dalignmm.c:2785:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2785 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2786:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2786 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                         ^~
Dalignmm.c:2786:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2786 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2787:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2787 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                         ^~
Dalignmm.c:2787:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2787 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2788:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2788 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                         ^~
Dalignmm.c:2788:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2788 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:2789:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2789 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                         ^~
Dalignmm.c:2789:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2789 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2790:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2790 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                         ^~
Dalignmm.c:2790:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2790 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:2791:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2791 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                         ^~
Dalignmm.c:2791:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2791 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:2792:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2792 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                         ^~
Dalignmm.c:2792:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2792 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c: In function 'D__align_variousdist':
Dalignmm.c:4478:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4478 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                         ^~
Dalignmm.c:4478:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4478 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4479:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4479 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                         ^~
Dalignmm.c:4479:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4479 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4480:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4480 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                         ^~
Dalignmm.c:4480:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4480 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4481:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4481 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                         ^~
Dalignmm.c:4481:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4481 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4483:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4483 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                         ^~
Dalignmm.c:4483:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4483 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4484:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4484 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                         ^~
Dalignmm.c:4484:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4484 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4485:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4485 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                         ^~
Dalignmm.c:4485:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4485 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4486:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4486 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                         ^~
Dalignmm.c:4486:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4486 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4487:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4487 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                         ^~
Dalignmm.c:4487:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4487 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4488:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4488 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                         ^~
Dalignmm.c:4488:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4488 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4489:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4489 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                         ^~
Dalignmm.c:4489:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4489 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4490:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4490 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                         ^~
Dalignmm.c:4490:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4490 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4491:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4491 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                         ^~
Dalignmm.c:4491:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4491 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:4492:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4492 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                         ^~
Dalignmm.c:4492:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4492 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:4648:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4648 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                         ^~
Dalignmm.c:4648:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4648 |                         if( gaplen1ibestkamo ) FreeGaplenCub( gaplen1ibestkamo ); gaplen1ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4649:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4649 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                         ^~
Dalignmm.c:4649:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4649 |                         if( gaplen2ibestkamo ) FreeGaplenCub( gaplen2ibestkamo ); gaplen2ibestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4650:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4650 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                         ^~
Dalignmm.c:4650:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4650 |                         if( gaplen1icurr ) FreeGaplenCub( gaplen1icurr ); gaplen1icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4651:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4651 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                         ^~
Dalignmm.c:4651:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4651 |                         if( gaplen2icurr ) FreeGaplenCub( gaplen2icurr ); gaplen2icurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4653:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4653 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                         ^~
Dalignmm.c:4653:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4653 |                         if( gaplen1jcurr ) FreeGaplenCub( gaplen1jcurr ); gaplen1jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4654:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4654 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                         ^~
Dalignmm.c:4654:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4654 |                         if( gaplen1jprev ) FreeGaplenCub( gaplen1jprev ); gaplen1jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4655:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4655 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                         ^~
Dalignmm.c:4655:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4655 |                         if( gaplen2jcurr ) FreeGaplenCub( gaplen2jcurr ); gaplen2jcurr = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4656:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4656 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                         ^~
Dalignmm.c:4656:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4656 |                         if( gaplen2jprev ) FreeGaplenCub( gaplen2jprev ); gaplen2jprev = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4657:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4657 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                         ^~
Dalignmm.c:4657:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4657 |                         if( gaplen1jbestkamo ) FreeGaplenCub( gaplen1jbestkamo ); gaplen1jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4658:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4658 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                         ^~
Dalignmm.c:4658:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4658 |                         if( gaplen2jbestkamo ) FreeGaplenCub( gaplen2jbestkamo ); gaplen2jbestkamo = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Dalignmm.c:4659:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4659 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                         ^~
Dalignmm.c:4659:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4659 |                         if( gaplen1jbest ) FreeGaplenCub( gaplen1jbest ); gaplen1jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4660:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4660 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                         ^~
Dalignmm.c:4660:75: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4660 |                         if( gaplen2jbest ) FreeGaplenCub( gaplen2jbest ); gaplen2jbest = NULL;
      |                                                                           ^~~~~~~~~~~~
Dalignmm.c:4661:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4661 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                         ^~
Dalignmm.c:4661:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4661 |                         if( gaplen1 ) FreeGaplenMtx( gaplen1, 1 ); gaplen1 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:4662:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4662 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                         ^~
Dalignmm.c:4662:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4662 |                         if( gaplen2 ) FreeGaplenMtx( gaplen2, 1 ); gaplen2 = NULL;
      |                                                                    ^~~~~~~
Dalignmm.c:5225:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5225 |                         if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL;
      |                         ^~
Dalignmm.c:5225:66: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5225 |                         if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL;
      |                                                                  ^~~~~~~~~
Dalignmm.c:5226:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5226 |                         if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL;
      |                         ^~
Dalignmm.c:5226:66: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5226 |                         if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL;
      |                                                                  ^~~~~~~~~
Dalignmm.c:5227:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5227 |                         if( nmask ) free( nmask ); nmask = NULL;
      |                         ^~
Dalignmm.c:5227:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5227 |                         if( nmask ) free( nmask ); nmask = NULL;
      |                                                    ^~~~~
Dalignmm.c:6121:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 6121 |         if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL;
      |         ^~
Dalignmm.c:6121:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 6121 |         if( masklist1 ) FreeIntMtx( masklist1 ); masklist1 = NULL;
      |                                                  ^~~~~~~~~
Dalignmm.c:6122:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 6122 |         if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL;
      |         ^~
Dalignmm.c:6122:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 6122 |         if( masklist2 ) FreeIntMtx( masklist2 ); masklist2 = NULL;
      |                                                  ^~~~~~~~~
Dalignmm.c:6123:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 6123 |         if( nmask ) free( nmask ); nmask = NULL;
      |         ^~
Dalignmm.c:6123:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 6123 |         if( nmask ) free( nmask ); nmask = NULL;
      |                                    ^~~~~
Dalignmm.c: In function 'D__align':
Dalignmm.c:3956:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 3956 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Dalignmm.c:2593:17: note: 'wmrecordspt' was declared here
 2593 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Dalignmm.c:3956:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 3956 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Dalignmm.c:2593:31: note: 'wmrecords1pt' was declared here
 2593 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Dalignmm.c:3931:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 3931 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Dalignmm.c:2593:46: note: 'prevwmrecordspt' was declared here
 2593 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Dalignmm.c:3959:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 3959 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Dalignmm.c:2594:14: note: 'warpipt' was declared here
 2594 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Dalignmm.c:3960:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 3960 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Dalignmm.c:2594:24: note: 'warpjpt' was declared here
 2594 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
Dalignmm.c: In function 'D__align_variousdist':
Dalignmm.c:5889:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 5889 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Dalignmm.c:4429:17: note: 'wmrecordspt' was declared here
 4429 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Dalignmm.c:5889:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 5889 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Dalignmm.c:4429:31: note: 'wmrecords1pt' was declared here
 4429 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Dalignmm.c:5864:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 5864 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_shift ) > wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Dalignmm.c:4429:46: note: 'prevwmrecordspt' was declared here
 4429 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Dalignmm.c:5892:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 5892 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Dalignmm.c:4430:14: note: 'warpipt' was declared here
 4430 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Dalignmm.c:5893:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 5893 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Dalignmm.c:4430:24: note: 'warpjpt' was declared here
 4430 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Falign.c
Falign.c: In function 'Fgetlag':
Falign.c:204:26: warning: variable 'nlen4' set but not used [-Wunused-but-set-variable]
  204 |         int nlen, nlen2, nlen4;
      |                          ^~~~~
Falign.c: In function 'Falign':
Falign.c:933:29: warning: unused variable 'p' [-Wunused-variable]
  933 |                         int p;
      |                             ^
Falign.c:776:26: warning: variable 'nlen4' set but not used [-Wunused-but-set-variable]
  776 |         int nlen, nlen2, nlen4;
      |                          ^~~~~
Falign.c: In function 'Falign_givenanchors':
Falign.c:1919:26: warning: variable 'nlen4' set but not used [-Wunused-but-set-variable]
 1919 |         int nlen, nlen2, nlen4;
      |                          ^~~~~
Falign.c: In function 'Falign_udpari_long':
Falign.c:2594:26: warning: variable 'nlen4' set but not used [-Wunused-but-set-variable]
 2594 |         int nlen, nlen2, nlen4;
      |                          ^~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Falign_localhom.c
Falign_localhom.c: In function 'Falign_localhom':
Falign_localhom.c:176:26: warning: variable 'nlen4' set but not used [-Wunused-but-set-variable]
  176 |         int nlen, nlen2, nlen4;
      |                          ^~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Galign11.c 
Galign11.c: In function 'G__align11psg':
Galign11.c:332:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  332 |                         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                         ^~
Galign11.c:332:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  332 |                         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                                                    ^~~~~
Galign11.c:333:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  333 |                         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                         ^~
Galign11.c:333:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  333 |                         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                                                    ^~~~~
Galign11.c:334:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  334 |                         if( w1 ) FreeFloatVec( w1 ); w1 = NULL;
      |                         ^~
Galign11.c:334:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  334 |                         if( w1 ) FreeFloatVec( w1 ); w1 = NULL;
      |                                                      ^~
Galign11.c:335:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  335 |                         if( w2 ) FreeFloatVec( w2 ); w2 = NULL;
      |                         ^~
Galign11.c:335:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  335 |                         if( w2 ) FreeFloatVec( w2 ); w2 = NULL;
      |                                                      ^~
Galign11.c:336:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  336 |                         if( match ) FreeFloatVec( match ); match = NULL;
      |                         ^~
Galign11.c:336:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  336 |                         if( match ) FreeFloatVec( match ); match = NULL;
      |                                                            ^~~~~
Galign11.c:337:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  337 |                         if( initverticalw ) FreeFloatVec( initverticalw ); initverticalw = NULL;
      |                         ^~
Galign11.c:337:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  337 |                         if( initverticalw ) FreeFloatVec( initverticalw ); initverticalw = NULL;
      |                                                                            ^~~~~~~~~~~~~
Galign11.c:338:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  338 |                         if( lastverticalw ) FreeFloatVec( lastverticalw ); lastverticalw = NULL;
      |                         ^~
Galign11.c:338:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  338 |                         if( lastverticalw ) FreeFloatVec( lastverticalw ); lastverticalw = NULL;
      |                                                                            ^~~~~~~~~~~~~
Galign11.c:340:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  340 |                         if( m ) FreeFloatVec( m ); m = NULL;
      |                         ^~
Galign11.c:340:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  340 |                         if( m ) FreeFloatVec( m ); m = NULL;
      |                                                    ^
Galign11.c:341:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  341 |                         if( mp ) FreeIntVec( mp ); mp = NULL;
      |                         ^~
Galign11.c:341:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  341 |                         if( mp ) FreeIntVec( mp ); mp = NULL;
      |                                                    ^~
Galign11.c:343:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  343 |                         if( mseq ) FreeCharMtx( mseq ); mseq = NULL;
      |                         ^~
Galign11.c:343:57: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  343 |                         if( mseq ) FreeCharMtx( mseq ); mseq = NULL;
      |                                                         ^~~~
Galign11.c:347:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  347 |                         if( doublework ) FreeFloatMtx( doublework ); doublework = NULL;
      |                         ^~
Galign11.c:347:70: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  347 |                         if( doublework ) FreeFloatMtx( doublework ); doublework = NULL;
      |                                                                      ^~~~~~~~~~
Galign11.c:348:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  348 |                         if( intwork ) FreeIntMtx( intwork ); intwork = NULL;
      |                         ^~
Galign11.c:348:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  348 |                         if( intwork ) FreeIntMtx( intwork ); intwork = NULL;
      |                                                              ^~~~~~~
Galign11.c:350:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  350 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
Galign11.c:350:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  350 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Galign11.c:352:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  352 |                         if( codonseq1 ) FreeIntMtx( codonseq1 ); codonseq1 = NULL;
      |                         ^~
Galign11.c:352:66: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  352 |                         if( codonseq1 ) FreeIntMtx( codonseq1 ); codonseq1 = NULL;
      |                                                                  ^~~~~~~~~
Galign11.c:353:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  353 |                         if( codonseq2 ) FreeIntMtx( codonseq2 ); codonseq2 = NULL;
      |                         ^~
Galign11.c:353:66: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  353 |                         if( codonseq2 ) FreeIntMtx( codonseq2 ); codonseq2 = NULL;
      |                                                                  ^~~~~~~~~
Galign11.c: In function 'G__align11':
Galign11.c:977:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  977 |                         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                         ^~
Galign11.c:977:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  977 |                         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                                                    ^~~~~
Galign11.c:978:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  978 |                         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                         ^~
Galign11.c:978:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  978 |                         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                                                    ^~~~~
Galign11.c:979:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  979 |                         if( w1 ) FreeFloatVec( w1 ); w1 = NULL;
      |                         ^~
Galign11.c:979:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  979 |                         if( w1 ) FreeFloatVec( w1 ); w1 = NULL;
      |                                                      ^~
Galign11.c:980:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  980 |                         if( w2 ) FreeFloatVec( w2 ); w2 = NULL;
      |                         ^~
Galign11.c:980:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  980 |                         if( w2 ) FreeFloatVec( w2 ); w2 = NULL;
      |                                                      ^~
Galign11.c:981:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  981 |                         if( match ) FreeFloatVec( match ); match = NULL;
      |                         ^~
Galign11.c:981:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  981 |                         if( match ) FreeFloatVec( match ); match = NULL;
      |                                                            ^~~~~
Galign11.c:982:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  982 |                         if( initverticalw ) FreeFloatVec( initverticalw ); initverticalw = NULL;
      |                         ^~
Galign11.c:982:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  982 |                         if( initverticalw ) FreeFloatVec( initverticalw ); initverticalw = NULL;
      |                                                                            ^~~~~~~~~~~~~
Galign11.c:983:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  983 |                         if( lastverticalw ) FreeFloatVec( lastverticalw ); lastverticalw = NULL;
      |                         ^~
Galign11.c:983:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  983 |                         if( lastverticalw ) FreeFloatVec( lastverticalw ); lastverticalw = NULL;
      |                                                                            ^~~~~~~~~~~~~
Galign11.c:985:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  985 |                         if( m ) FreeFloatVec( m ); m = NULL;
      |                         ^~
Galign11.c:985:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  985 |                         if( m ) FreeFloatVec( m ); m = NULL;
      |                                                    ^
Galign11.c:986:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  986 |                         if( mp ) FreeIntVec( mp ); mp = NULL;
      |                         ^~
Galign11.c:986:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  986 |                         if( mp ) FreeIntVec( mp ); mp = NULL;
      |                                                    ^~
Galign11.c:988:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  988 |                         if( mseq ) FreeCharMtx( mseq ); mseq = NULL;
      |                         ^~
Galign11.c:988:57: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  988 |                         if( mseq ) FreeCharMtx( mseq ); mseq = NULL;
      |                                                         ^~~~
Galign11.c:992:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  992 |                         if( doublework ) FreeFloatMtx( doublework ); doublework = NULL;
      |                         ^~
Galign11.c:992:70: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  992 |                         if( doublework ) FreeFloatMtx( doublework ); doublework = NULL;
      |                                                                      ^~~~~~~~~~
Galign11.c:993:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  993 |                         if( intwork ) FreeIntMtx( intwork ); intwork = NULL;
      |                         ^~
Galign11.c:993:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  993 |                         if( intwork ) FreeIntMtx( intwork ); intwork = NULL;
      |                                                              ^~~~~~~
Galign11.c:995:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  995 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
Galign11.c:995:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  995 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Galign11.c: In function 'Atracking':
Galign11.c:261:15: warning: 'wm' may be used uninitialized [-Wmaybe-uninitialized]
  261 |         return( wm );
      |               ^
Galign11.c:107:16: note: 'wm' was declared here
  107 |         double wm, g;
      |                ^~
Galign11.c: In function 'G__align11psg':
Galign11.c:815:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
  815 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Galign11.c:323:17: note: 'wmrecordspt' was declared here
  323 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Galign11.c:815:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
  815 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Galign11.c:323:31: note: 'wmrecords1pt' was declared here
  323 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Galign11.c:787:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
  787 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_tmp )> wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Galign11.c:323:46: note: 'prevwmrecordspt' was declared here
  323 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Galign11.c:822:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
  822 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Galign11.c:324:14: note: 'warpipt' was declared here
  324 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Galign11.c:823:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
  823 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Galign11.c:324:24: note: 'warpjpt' was declared here
  324 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
Galign11.c: In function 'G__align11':
Galign11.c:1376:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1376 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Galign11.c:967:17: note: 'wmrecordspt' was declared here
  967 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Galign11.c:1376:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
 1376 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Galign11.c:967:31: note: 'wmrecords1pt' was declared here
  967 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Galign11.c:1348:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
 1348 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_tmp )> wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Galign11.c:967:46: note: 'prevwmrecordspt' was declared here
  967 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Galign11.c:1383:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
 1383 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Galign11.c:968:14: note: 'warpipt' was declared here
  968 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Galign11.c:1384:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
 1384 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Galign11.c:968:24: note: 'warpjpt' was declared here
  968 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c Lalign11.c 
Lalign11.c: In function 'L__align11':
Lalign11.c:285:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  285 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
Lalign11.c:285:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  285 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Lalign11.c:340:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  340 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
Lalign11.c:340:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  340 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Lalign11.c: In function 'L__align11_noalign':
Lalign11.c:807:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  807 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
Lalign11.c:807:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  807 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Lalign11.c:845:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  845 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
Lalign11.c:845:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  845 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
Lalign11.c: In function 'L__align11':
Lalign11.c:629:53: warning: 'wmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
  629 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                                     ^~~~~~~~~~~~
Lalign11.c:262:17: note: 'wmrecordspt' was declared here
  262 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                 ^~~~~~~~~~~
Lalign11.c:629:37: warning: 'wmrecords1pt' may be used uninitialized [-Wmaybe-uninitialized]
  629 |                                 if( *wmrecords1pt > *wmrecordspt )
      |                                     ^~~~~~~~~~~~~
Lalign11.c:262:31: note: 'wmrecords1pt' was declared here
  262 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                               ^~~~~~~~~~~~
Lalign11.c:601:41: warning: 'prevwmrecordspt' may be used uninitialized [-Wmaybe-uninitialized]
  601 |                                 if( ( g=*prevwmrecordspt++ + fpenalty_tmp )> wm ) // naka ha osokute kamawanai
      |                                         ^~~~~~~~~~~~~~~~~~
Lalign11.c:262:46: note: 'prevwmrecordspt' was declared here
  262 |         double *wmrecordspt, *wmrecords1pt, *prevwmrecordspt;
      |                                              ^~~~~~~~~~~~~~~
Lalign11.c:636:51: warning: 'warpipt' may be used uninitialized [-Wmaybe-uninitialized]
  636 |                                         *warpipt  = *(warpipt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Lalign11.c:263:14: note: 'warpipt' was declared here
  263 |         int *warpipt, *warpjpt;
      |              ^~~~~~~
Lalign11.c:637:51: warning: 'warpjpt' may be used uninitialized [-Wmaybe-uninitialized]
  637 |                                         *warpjpt  = *(warpjpt-1);
      |                                         ~~~~~~~~~~^~~~~~~~~~~~~~
Lalign11.c:263:24: note: 'warpjpt' was declared here
  263 |         int *warpipt, *warpjpt;
      |                        ^~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c genalign11.c 
genalign11.c: In function 'genL__align11':
genalign11.c:190:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  190 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
genalign11.c:190:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  190 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
genalign11.c:234:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  234 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                         ^~
genalign11.c:234:83: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  234 |                         if( amino_dynamicmtx ) FreeDoubleMtx( amino_dynamicmtx ); amino_dynamicmtx = NULL;
      |                                                                                   ^~~~~~~~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c MSalignmm.c 
MSalignmm.c: In function 'MSalignmm_rec':
MSalignmm.c:1911:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1911 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                 ^~~
MSalignmm.c:1911:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1911 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                                                            ^~~~
MSalignmm.c:1922:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1922 |                 for( i=0,j=len; i<l; i++,j++ ) mgt1[j] = '-'; mgt1[j] = 0;
      |                 ^~~
MSalignmm.c:1922:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1922 |                 for( i=0,j=len; i<l; i++,j++ ) mgt1[j] = '-'; mgt1[j] = 0;
      |                                                               ^~~~
MSalignmm.c:1923:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1923 |                 for( i=0,j=len; i<l; i++,j++ ) mgt2[j] = 'o'; mgt2[j] = 0;
      |                 ^~~
MSalignmm.c:1923:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1923 |                 for( i=0,j=len; i<l; i++,j++ ) mgt2[j] = 'o'; mgt2[j] = 0;
      |                                                               ^~~~
MSalignmm.c:1934:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1934 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                 ^~~
MSalignmm.c:1934:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1934 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                                                            ^~~~
MSalignmm.c:1945:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1945 |                 for( i=0,j=len; i<l; i++,j++ ) mgt1[j] = 'o'; mgt1[j] = 0;
      |                 ^~~
MSalignmm.c:1945:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1945 |                 for( i=0,j=len; i<l; i++,j++ ) mgt1[j] = 'o'; mgt1[j] = 0;
      |                                                               ^~~~
MSalignmm.c:1946:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1946 |                 for( i=0,j=len; i<l; i++,j++ ) mgt2[j] = '-'; mgt2[j] = 0;
      |                 ^~~
MSalignmm.c:1946:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1946 |                 for( i=0,j=len; i<l; i++,j++ ) mgt2[j] = '-'; mgt2[j] = 0;
      |                                                               ^~~~
MSalignmm.c:1000:13: warning: variable 'lasti' set but not used [-Wunused-but-set-variable]
 1000 |         int lasti, lastj, imid;
      |             ^~~~~
MSalignmm.c: In function 'MSalignmm_rec_variousdist':
MSalignmm.c:3803:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 3803 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                 ^~~
MSalignmm.c:3803:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 3803 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                                                            ^~~~
MSalignmm.c:3824:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 3824 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                 ^~~
MSalignmm.c:3824:60: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 3824 |                 for( i=0; i<l; i++ ) gaps[i] = *newgapstr; gaps[i] = 0;
      |                                                            ^~~~
MSalignmm.c:2889:13: warning: variable 'lasti' set but not used [-Wunused-but-set-variable]
 2889 |         int lasti, lastj, imid;
      |             ^~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c fftFunctions.c
fftFunctions.c: In function 'keika':
fftFunctions.c:10:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   10 |         if( current == 0 )
      |         ^~
fftFunctions.c:13:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
   13 |                 fprintf( stderr, "\b\b\b\b\b\b\b\b" );
      |                 ^~~~~~~
fftFunctions.c: In function 'alignableReagion':
fftFunctions.c:209:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  209 |                 if( stra ) FreeDoubleVec( stra ); stra = NULL;
      |                 ^~
fftFunctions.c:209:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  209 |                 if( stra ) FreeDoubleVec( stra ); stra = NULL;
      |                                                   ^~~~
fftFunctions.c:210:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  210 |                 if( prf1 ) FreeDoubleVec( prf1 ); prf1 = NULL;
      |                 ^~
fftFunctions.c:210:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  210 |                 if( prf1 ) FreeDoubleVec( prf1 ); prf1 = NULL;
      |                                                   ^~~~
fftFunctions.c:211:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  211 |                 if( prf2 ) FreeDoubleVec( prf2 ); prf2 = NULL;
      |                 ^~
fftFunctions.c:211:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  211 |                 if( prf2 ) FreeDoubleVec( prf2 ); prf2 = NULL;
      |                                                   ^~~~
fftFunctions.c:212:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  212 |                 if( hat1 ) FreeIntVec( hat1 ); hat1 = NULL;
      |                 ^~
fftFunctions.c:212:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  212 |                 if( hat1 ) FreeIntVec( hat1 ); hat1 = NULL;
      |                                                ^~~~
fftFunctions.c:213:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  213 |                 if( hat2 ) FreeIntVec( hat2 ); hat2 = NULL;
      |                 ^~
fftFunctions.c:213:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  213 |                 if( hat2 ) FreeIntVec( hat2 ); hat2 = NULL;
      |                                                ^~~~
fftFunctions.c: In function 'blockAlign2':
fftFunctions.c:404:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  404 |                         if( result1 ) free( result1 ); result1 = NULL;
      |                         ^~
fftFunctions.c:404:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  404 |                         if( result1 ) free( result1 ); result1 = NULL;
      |                                                        ^~~~~~~
fftFunctions.c:405:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  405 |                         if( result2 ) free( result2 ); result2 = NULL;
      |                         ^~
fftFunctions.c:405:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  405 |                         if( result2 ) free( result2 ); result2 = NULL;
      |                                                        ^~~~~~~
fftFunctions.c:406:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  406 |                         if( ocut1 ) free( ocut1 ); ocut1 = NULL;
      |                         ^~
fftFunctions.c:406:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  406 |                         if( ocut1 ) free( ocut1 ); ocut1 = NULL;
      |                                                    ^~~~~
fftFunctions.c:407:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  407 |                         if( ocut2 ) free( ocut2 ); ocut2 = NULL;
      |                         ^~
fftFunctions.c:407:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  407 |                         if( ocut2 ) free( ocut2 ); ocut2 = NULL;
      |                                                    ^~~~~
fftFunctions.c:408:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  408 |                         if( track ) FreeIntMtx( track ); track = NULL;
      |                         ^~
fftFunctions.c:408:58: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  408 |                         if( track ) FreeIntMtx( track ); track = NULL;
      |                                                          ^~~~~
fftFunctions.c:409:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  409 |                         if( crossscore ) FreeDoubleMtx( crossscore ); crossscore = NULL;
      |                         ^~
fftFunctions.c:409:71: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  409 |                         if( crossscore ) FreeDoubleMtx( crossscore ); crossscore = NULL;
      |                                                                       ^~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c fft.c 
fft.c: In function 'fft':
fft.c:55:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   55 |                         if (bitrev) free(bitrev); bitrev = NULL;
      |                         ^~
fft.c:55:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
   55 |                         if (bitrev) free(bitrev); bitrev = NULL;
      |                                                   ^~~~~~
fft.c:56:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
   56 |                         if (sintbl) free(sintbl); sintbl = NULL;
      |                         ^~
fft.c:56:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
   56 |                         if (sintbl) free(sintbl); sintbl = NULL;
      |                                                   ^~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c tditeration.c
tditeration.c: In function 'Writeoptions':
tditeration.c:208:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  208 |     if( weight && !utree )
      |     ^~
tditeration.c:211:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  211 |         if( treemethod == 'n' )
      |         ^~
tditeration.c: In function 'athread':
tditeration.c:1032:56: warning: variable 'totalwm' set but not used [-Wunused-but-set-variable]
 1032 |                                                 double totalwm;
      |                                                        ^~~~~~~
tditeration.c: In function 'TreeDependentIteration':
tditeration.c:2142:56: warning: variable 'totalwm' set but not used [-Wunused-but-set-variable]
 2142 |                                                 double totalwm;
      |                                                        ^~~~~~~
tditeration.c: In function 'athread':
tditeration.c:694:33: warning: 'rnapairboth' may be used uninitialized [-Wmaybe-uninitialized]
  694 |                                 freelocalarrays
      |                                 ^~~~~~~~~~~~~~~
  695 |                                 (
      |                                 ~
  696 |                                         tscorehistory,
      |                                         ~~~~~~~~~~~~~~
  697 |                                         grouprna1, grouprna2,
      |                                         ~~~~~~~~~~~~~~~~~~~~~
  698 |                                         rnapairboth,
      |                                         ~~~~~~~~~~~~
  699 |                                         indication1, indication2,
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~
  700 |                                         distarr,
      |                                         ~~~~~~~~
  701 |                                         effarr, effarrforlocalhom, effarr1, effarr2,
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  702 |                                         mseq1, mseq2,
      |                                         ~~~~~~~~~~~~~
  703 |                                         localcopy,
      |                                         ~~~~~~~~~~
  704 |                                         gapmap1, gapmap2,
      |                                         ~~~~~~~~~~~~~~~~~
  705 |                                         effarr1_kozo, effarr2_kozo, effarr_kozo,
      |                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  706 |                                         memlist, pairbuf,
      |                                         ~~~~~~~~~~~~~~~~~
  707 |                                         localhomshrink,
      |                                         ~~~~~~~~~~~~~~~
  708 |                                         swaplist,
      |                                         ~~~~~~~~~
  709 |                                         smalldistmtx,
      |                                         ~~~~~~~~~~~~~
  710 |                                         scoringmatrices,
      |                                         ~~~~~~~~~~~~~~~~
  711 |                                         eff1s, eff2s,
      |                                         ~~~~~~~~~~~~~
  712 |                                         whichmtx
      |                                         ~~~~~~~~
  713 |                                 );
      |                                 ~
tditeration.c:383:18: note: 'rnapairboth' was declared here
  383 |         RNApair *rnapairboth;
      |                  ^~~~~~~~~~~
tditeration.c:878:49: warning: 'localhomshrink' may be used uninitialized [-Wmaybe-uninitialized]
  878 |                                                 msshrinklocalhom_fast_half( memlist[0], memlist[1], localhomtable, localhomshrink );
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tditeration.c:384:21: note: 'localhomshrink' was declared here
  384 |         LocalHom ***localhomshrink;
      |                     ^~~~~~~~~~~~~~
tditeration.c: In function 'TreeDependentIteration':
tditeration.c:1493:44: warning: 'candidates' may be used uninitialized [-Wmaybe-uninitialized]
 1493 |                         targ[i].candidates = candidates;
      |                         ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
tditeration.c:1452:25: note: 'candidates' was declared here
 1452 |                 char ***candidates;
      |                         ^~~~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c dvtditr.c
dvtditr.c: In function 'main':
dvtditr.c:435:13: warning: variable 'returnvalue' set but not used [-Wunused-but-set-variable]
  435 |         int returnvalue;
      |             ^~~~~~~~~~~
dvtditr.c:1020:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1020 |                                 system( "cp infile.tree GuideTree" ); // tekitou
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dvtditr.c:984:43: warning: 'insubtable' may be used uninitialized [-Wmaybe-uninitialized]
  984 |                                 insubtable[subtable[i][j]] = 1;
      |                                           ^
dvtditr.c:451:14: note: 'insubtable' was declared here
  451 |         int *insubtable;
      |              ^~~~~~~~~~
dvtditr.c:1076:17: warning: 'preservegaps' may be used uninitialized [-Wmaybe-uninitialized]
 1076 |                 free( preservegaps );
      |                 ^~~~~~~~~~~~~~~~~~~~
dvtditr.c:452:14: note: 'preservegaps' was declared here
  452 |         int *preservegaps;
      |              ^~~~~~~~~~~~
dvtditr.c:1069:25: warning: 'subalnpt' may be used uninitialized [-Wmaybe-uninitialized]
 1069 |                         commongappick( j, subalnpt[i] );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dvtditr.c:453:17: note: 'subalnpt' was declared here
  453 |         char ***subalnpt;
      |                 ^~~~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c defs.c
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c SAalignmm.c -o SAalignmm.o
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c treeOperation.c
treeOperation.c: In function 'distFromABranch_rec':
treeOperation.c:492:24: warning: variable 'dir_pa' set but not used [-Wunused-but-set-variable]
  492 |         int dir_ch[3], dir_pa;
      |                        ^~~~~~
treeOperation.c: In function 'weightFromABranch_rec':
treeOperation.c:575:24: warning: variable 'dir_pa' set but not used [-Wunused-but-set-variable]
  575 |         int dir_ch[3], dir_pa;
      |                        ^~~~~~
treeOperation.c: In function 'assignstrweight_rec':
treeOperation.c:645:24: warning: variable 'dir_pa' set but not used [-Wunused-but-set-variable]
  645 |         int dir_ch[3], dir_pa;
      |                        ^~~~~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c addfunctions.c
addfunctions.c: In function 'profilealignment2':
addfunctions.c:38:16: warning: variable 'newlen' set but not used [-Wunused-but-set-variable]
   38 |         int i, newlen;
      |                ^~~~~~
addfunctions.c: In function 'restoregaponlysites':
addfunctions.c:1913:16: warning: unused variable 'j' [-Wunused-variable]
 1913 |         int i, j, p;
      |                ^
gcc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o   -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
In function 'generatesubalignmentstable',
    inlined from 'main' at dvtditr.c:815:7:
mltaln9.c:15290:23: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
15290 |         distfromtip = calloc( nseq, sizeof( double ) );
      |                       ^
/usr/include/stdlib.h: In function 'main':
/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c dndfast7.c
dndfast7.c: In function 'main':
dndfast7.c:326:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  326 |         system( com );
      |         ^~~~~~~~~~~~~
gcc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -c -o dndblast.o dndblast.c
dndblast.c: In function 'main':
dndblast.c:201:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  201 |                         system( com );
      |                         ^~~~~~~~~~~~~
dndblast.c:382:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  382 |         system( com );
      |         ^~~~~~~~~~~~~
gcc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c sextet5.c
gcc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c mafft-distance.c
gcc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c MSalign11.c 
MSalign11.c: In function 'backdp':
MSalign11.c:133:13: warning: variable 'mpi' set but not used [-Wunused-but-set-variable]
  133 |         int mpi;
      |             ^~~
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c suboptalign11.c 
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c pairlocalalignmain.c
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c pairlocalalign.c
pairlocalalign.c: In function 'calllast_once':
pairlocalalign.c:1056:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1056 |                 system( command );
      |                 ^~~~~~~~~~~~~~~~~
pairlocalalign.c:1092:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1092 |                 system( command );
      |                 ^~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'readlastresx':
pairlocalalign.c:608:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  608 |                 fgets( gett, 9999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'calllast_fast':
pairlocalalign.c:981:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  981 |                 system( command );
      |                 ^~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'lastcallthread':
pairlocalalign.c:872:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  872 |                                 system( command );
      |                                 ^~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'readlastresx_singleq':
pairlocalalign.c:374:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  374 |                 fgets( gett, 9999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'readhat4':
pairlocalalign.c:1532:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1532 |         fgets( oneline, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1544:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1544 |                 fgets( oneline, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'recalllara':
pairlocalalign.c:1245:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1245 |         fgets( com, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'callmxscarna_giving_bpp':
pairlocalalign.c:1408:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1408 |         system( com );
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1410:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1410 |         system( com );
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1430:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1430 |         system( com ); // for cygwin, wakaran
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1451:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1451 |         system( com ); // for cygwin, wakaran
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1465:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1465 |         system( com ); // for cygwin, wakaran
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1485:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1485 |         fgets( com, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1487:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1487 |         fgets( com, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'calldafs_giving_bpp':
pairlocalalign.c:1291:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1291 |         system( com );
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1293:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1293 |         system( com );
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1313:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1313 |         system( com ); // for cygwin, wakaran
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1334:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1334 |         system( com ); // for cygwin, wakaran
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1344:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 1344 |         system( com ); // for cygwin, wakaran
      |         ^~~~~~~~~~~~~
pairlocalalign.c:1364:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1364 |         fgets( com, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1366:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1366 |         fgets( com, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1368:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
 1368 |         fgets( com, 999, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'pairalign_node':
pairlocalalign.c:3467:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 3467 |         system( "rm -rf hat3dir" ); // toriaezu
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:3468:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 3468 |         system( "mkdir hat3dir" ); // toriaezu
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:3473:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 3473 |                 system( fn );
      |                 ^~~~~~~~~~~~
pairlocalalign.c: In function 'putlocalhom_last.constprop.0.isra.0':
pairlocalalign.c:219:50: warning: 'localhompt0' may be used uninitialized [-Wmaybe-uninitialized]
  219 |                         for( tmppt2=localhompt0; tmppt2; tmppt2=tmppt2->next )
      |                                                  ^~~~~~
pairlocalalign.c:140:19: note: 'localhompt0' was declared here
  140 |         LocalHom *localhompt0;
      |                   ^~~~~~~~~~~
pairlocalalign.c: In function 'athread':
pairlocalalign.c:2237:66: warning: 'dumseq1' may be used uninitialized [-Wmaybe-uninitialized]
 2237 |                                                         pscore = genL__align11( n_dis_consweight_multi, dumseq1, dumseq2, alloclen, &dum1, &dum2 ); // uwagaki
      |                                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1955:58: note: 'dumseq1' was declared here
 1955 |         char **mseq1, **mseq2, **distseq1, **distseq2, **dumseq1, **dumseq2;
      |                                                          ^~~~~~~
pairlocalalign.c:2237:66: warning: 'dumseq2' may be used uninitialized [-Wmaybe-uninitialized]
 2237 |                                                         pscore = genL__align11( n_dis_consweight_multi, dumseq1, dumseq2, alloclen, &dum1, &dum2 ); // uwagaki
      |                                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c:1955:69: note: 'dumseq2' was declared here
 1955 |         char **mseq1, **mseq2, **distseq1, **distseq2, **dumseq1, **dumseq2;
      |                                                                     ^~~~~~~
pairlocalalign.c: In function 'pairlocalalign':
pairlocalalign.c:3212:17: warning: 'infp' may be used uninitialized [-Wmaybe-uninitialized]
 3212 |                 fclose( infp );
      |                 ^~~~~~~~~~~~~~
pairlocalalign.c:3100:15: note: 'infp' was declared here
 3100 |         FILE *infp;
      |               ^~~~
In function 'pairalign',
    inlined from 'pairlocalalign' at pairlocalalign.c:3257:2:
pairlocalalign.c:2776:82: warning: 'dumseq1' may be used uninitialized [-Wmaybe-uninitialized]
 2776 |                                                                         pscore = genL__align11( n_dis_consweight_multi, dumseq1, dumseq2, alloclen, &dum1, &dum2 ); // uwagaki
      |                                                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'pairlocalalign':
pairlocalalign.c:2405:16: note: 'dumseq1' was declared here
 2405 |         char **dumseq1, **dumseq2;
      |                ^~~~~~~
In function 'pairalign',
    inlined from 'pairlocalalign' at pairlocalalign.c:3257:2:
pairlocalalign.c:2776:82: warning: 'dumseq2' may be used uninitialized [-Wmaybe-uninitialized]
 2776 |                                                                         pscore = genL__align11( n_dis_consweight_multi, dumseq1, dumseq2, alloclen, &dum1, &dum2 ); // uwagaki
      |                                                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairlocalalign.c: In function 'pairlocalalign':
pairlocalalign.c:2405:27: note: 'dumseq2' was declared here
 2405 |         char **dumseq1, **dumseq2;
      |                           ^~~~~~~
gcc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairlocalalignmain.o pairlocalalign.o defs.o fft.o fftFunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
In function 'Atracking',
    inlined from 'A__align.constprop' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c multi2hat3s.c
multi2hat3s.c: In function 'pairalign':
multi2hat3s.c:143:15: warning: variable 'aseq' set but not used [-Wunused-but-set-variable]
  143 |         char *aseq;
      |               ^~~~
multi2hat3s.c:142:24: warning: variable 'effarr2' set but not used [-Wunused-but-set-variable]
  142 |         static double *effarr2 = NULL;
      |                        ^~~~~~~
gcc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c pairash.c
pairash.c: In function 'pairalign':
pairash.c:1027:20: warning: variable 'clus2' set but not used [-Wunused-but-set-variable]
 1027 |         int clus1, clus2;
      |                    ^~~~~
pairash.c:1027:13: warning: variable 'clus1' set but not used [-Wunused-but-set-variable]
 1027 |         int clus1, clus2;
      |             ^~~~~
pairash.c: In function 'prepareash':
pairash.c:639:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  639 |                 fgets( line, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:681:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  681 |                 fgets( line, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'callrash':
pairash.c:485:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  485 |                 system( com );
      |                 ^~~~~~~~~~~~~
pairash.c: In function 'readrash':
pairash.c:277:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  277 |                 fgets( line, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:284:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  284 |                         fgets( line, 999, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:289:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  289 |                         fgets( line, 999, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:294:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  294 |                         fgets( line, 999, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'preparetmalign':
pairash.c:530:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  530 |                 fgets( line, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:576:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  576 |                 fgets( line, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:587:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  587 |                         system( command );
      |                         ^~~~~~~~~~~~~~~~~
pairash.c: In function 'checkcbeta':
pairash.c:321:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  321 |                 fgets( linec, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'calltmalign':
pairash.c:347:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  347 |                 system( com );
      |                 ^~~~~~~~~~~~~
pairash.c:356:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  356 |                         fgets( com, 100, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'readtmalign':
pairash.c:228:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  228 |                 fgets( line, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
pairash.c:232:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  232 |         fgets( line, nlenmax*2, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairash.c:235:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  235 |         fgets( line, nlenmax*2, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairash.c:238:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  238 |         fgets( line, nlenmax*2, fp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'callrash.isra.0':
pairash.c:428:43: warning: '.' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=]
  428 |                 sprintf( cachefile, "%s/%s.%s.rash", cachedir, fname1, fname2 );
      |                                           ^
In file included from /usr/include/stdio.h:964,
                 from mltaln.h:12,
                 from pairash.c:1:
In function 'sprintf',
    inlined from 'callrash.isra.0' at pairash.c:428:3:
/usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output 8 or more bytes (assuming 10007) into a destination of size 10000
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
pairash.c: In function 'callrash.isra.0':
pairash.c:484:36: warning: '%s' directive writing up to 9999 bytes into a region of size 9996 [-Wformat-overflow=]
  484 |                 sprintf( com, "cat %s > %s.rashout", cachefile, pairid );
      |                                    ^~                ~~~~~~~~~
In function 'sprintf',
    inlined from 'callrash.isra.0' at pairash.c:484:3:
/usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 16 and 11014 bytes into a destination of size 10000
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
pairash.c: In function 'calltmalign.isra.0':
pairash.c:346:41: warning: '%s' directive writing up to 9999 bytes into a region of size 9991 [-Wformat-overflow=]
  346 |                 sprintf( com, "mkdir -p %s", cachedir );
      |                                         ^~   ~~~~~~~~
In function 'sprintf',
    inlined from 'calltmalign.isra.0' at pairash.c:346:3:
/usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output between 10 and 10009 bytes into a destination of size 10000
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
pairash.c: In function 'calltmalign.isra.0':
pairash.c:349:45: warning: '-' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=]
  349 |                 sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 );
      |                                             ^
In function 'sprintf',
    inlined from 'calltmalign.isra.0' at pairash.c:349:3:
/usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output 3 or more bytes (assuming 10002) into a destination of size 10000
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
pairash.c: In function 'preparetmalign.constprop.0':
pairash.c:586:50: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=]
  586 |                         sprintf( command, "cp %s %s.pdb", sline, fname );
      |                                                  ^~              ~~~~~
In function 'sprintf',
    inlined from 'preparetmalign.constprop.0' at pairash.c:586:4:
/usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output 9 or more bytes (assuming 1008) into a destination of size 1000
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
pairash.c: In function 'preparetmalign.constprop.0':
pairash.c:588:65: warning: '%s' directive writing up to 999 bytes into a region of size 983 [-Wformat-overflow=]
  588 |                         sprintf( command, "perl \"%s/clean.pl\" %s.pdb", whereispairalign, fname );
      |                                                                 ^~                         ~~~~~
In function 'sprintf',
    inlined from 'preparetmalign.constprop.0' at pairash.c:588:4:
/usr/include/bits/stdio2.h:30:10: note: '__sprintf_chk' output 22 or more bytes (assuming 1021) into a destination of size 1000
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
In function 'pairalign',
    inlined from 'main' at pairash.c:1425:2:
pairash.c:1092:17: warning: 'checkseq' may be used uninitialized [-Wmaybe-uninitialized]
 1092 |                 strcpy( checkseq[i], seq[i] );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pairash.c: In function 'main':
pairash.c:1041:16: note: 'checkseq' was declared here
 1041 |         char **checkseq;
      |                ^~~~~~~~
gcc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairash.o defs.o fft.o fftFunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c addsingle.c
addsingle.c: In function 'addsinglethread':
addsingle.c:2038:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2038 |                 if( mergeoralign ) free( mergeoralign );  mergeoralign = NULL;
      |                 ^~
addsingle.c:2038:59: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2038 |                 if( mergeoralign ) free( mergeoralign );  mergeoralign = NULL;
      |                                                           ^~~~~~~~~~~~
addsingle.c:2039:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2039 |                 if( nogaplenjusttodecideaddhereornot ) free( nogaplenjusttodecideaddhereornot ); nogaplenjusttodecideaddhereornot = NULL;
      |                 ^~
addsingle.c:2039:98: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2039 |                 if( nogaplenjusttodecideaddhereornot ) free( nogaplenjusttodecideaddhereornot ); nogaplenjusttodecideaddhereornot = NULL;
      |                                                                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
addsingle.c:2040:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2040 |                 if( alnleninnode ) free( alnleninnode ); alnleninnode = NULL;
      |                 ^~
addsingle.c:2040:58: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2040 |                 if( alnleninnode ) free( alnleninnode ); alnleninnode = NULL;
      |                                                          ^~~~~~~~~~~~
addsingle.c:2041:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2041 |                 if( tmpseq ) free( tmpseq ); tmpseq = NULL;
      |                 ^~
addsingle.c:2041:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2041 |                 if( tmpseq ) free( tmpseq ); tmpseq = NULL;
      |                                              ^~~~~~
addsingle.c:2042:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2042 |                 if( bseq ) FreeCharMtx( bseq ); bseq = NULL;
      |                 ^~
addsingle.c:2042:49: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2042 |                 if( bseq ) FreeCharMtx( bseq ); bseq = NULL;
      |                                                 ^~~~
addsingle.c:2043:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2043 |                 if( namec ) free( namec ); namec = NULL;
      |                 ^~
addsingle.c:2043:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2043 |                 if( namec ) free( namec ); namec = NULL;
      |                                            ^~~~~
addsingle.c:2044:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2044 |                 if( nlenc ) free( nlenc  ); nlenc = NULL;
      |                 ^~
addsingle.c:2044:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2044 |                 if( nlenc ) free( nlenc  ); nlenc = NULL;
      |                                             ^~~~~
addsingle.c:2045:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2045 |                 if( depc ) free( depc ); depc = NULL;
      |                 ^~
addsingle.c:2045:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2045 |                 if( depc ) free( depc ); depc = NULL;
      |                                          ^~~~
addsingle.c:2046:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2046 |                 if( topolc ) FreeIntCub( topolc ); topolc = NULL;
      |                 ^~
addsingle.c:2046:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2046 |                 if( topolc ) FreeIntCub( topolc ); topolc = NULL;
      |                                                    ^~~~~~
addsingle.c:2047:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2047 |                 if( lenc ) FreeFloatMtx( lenc ); lenc = NULL;
      |                 ^~
addsingle.c:2047:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2047 |                 if( lenc ) FreeFloatMtx( lenc ); lenc = NULL;
      |                                                  ^~~~
addsingle.c:2048:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2048 |                 if( effc ) FreeDoubleVec( effc ); effc = NULL;
      |                 ^~
addsingle.c:2048:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2048 |                 if( effc ) FreeDoubleVec( effc ); effc = NULL;
      |                                                   ^~~~
addsingle.c:2049:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2049 |                 if( memlist0 ) free( memlist0 ); memlist0 = NULL;
      |                 ^~
addsingle.c:2049:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2049 |                 if( memlist0 ) free( memlist0 ); memlist0 = NULL;
      |                                                  ^~~~~~~~
addsingle.c:2050:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2050 |                 if( memlist1 ) free( memlist1 ); memlist1 = NULL;
      |                 ^~
addsingle.c:2050:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2050 |                 if( memlist1 ) free( memlist1 ); memlist1 = NULL;
      |                                                  ^~~~~~~~
addsingle.c:2051:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2051 |                 if( addmem ) free( addmem ); addmem = NULL;
      |                 ^~
addsingle.c:2051:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2051 |                 if( addmem ) free( addmem ); addmem = NULL;
      |                                              ^~~~~~
addsingle.c:2052:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2052 |                 if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                 ^~
addsingle.c:2052:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2052 |                 if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                                            ^~~~~
addsingle.c:2053:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2053 |                 if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                 ^~
addsingle.c:2053:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2053 |                 if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                                            ^~~~~
addsingle.c:1635:24: warning: variable 'pscore' set but not used [-Wunused-but-set-variable]
 1635 |                 double pscore;
      |                        ^~~~~~
addsingle.c:1634:26: warning: unused variable 'difflist' [-Wunused-variable]
 1634 |                 GapPos **difflist = targ->difflist;
      |                          ^~~~~~~~
addsingle.c: In function 'main':
addsingle.c:3835:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3835 |         if( addbk ) FreeCharMtx( addbk ); addbk = NULL;
      |         ^~
addsingle.c:3835:43: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3835 |         if( addbk ) FreeCharMtx( addbk ); addbk = NULL;
      |                                           ^~~~~
addsingle.c:3848:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3848 |         if( originalgaps ) free( originalgaps ); originalgaps = NULL;
      |         ^~
addsingle.c:3848:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3848 |         if( originalgaps ) free( originalgaps ); originalgaps = NULL;
      |                                                  ^~~~~~~~~~~~
addsingle.c:2974:25: warning: variable 'len_kozo' set but not used [-Wunused-but-set-variable]
 2974 |         static double **len_kozo;
      |                         ^~~~~~~~
addsingle.c:2972:23: warning: variable 'topol_kozo' set but not used [-Wunused-but-set-variable]
 2972 |         static int ***topol_kozo;
      |                       ^~~~~~~~~~
addsingle.c:2969:24: warning: variable 'eff_kozo' set but not used [-Wunused-but-set-variable]
 2969 |         static double *eff_kozo, *eff_kozo_mapped = NULL;
      |                        ^~~~~~~~
addsingle.c:2968:35: warning: variable 'iscore_kozo' set but not used [-Wunused-but-set-variable]
 2968 |         static double **iscore, **iscore_kozo;
      |                                   ^~~~~~~~~~~
addsingle.c:3532:33: warning: 'addtree' may be used uninitialized [-Wmaybe-uninitialized]
 3532 |                 targ[0].addtree = addtree;
      |                 ~~~~~~~~~~~~~~~~^~~~~~~~~
addsingle.c:3005:18: note: 'addtree' was declared here
 3005 |         Addtree *addtree;
      |                  ^~~~~~~
gcc -o addsingle mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o addsingle.o defs.o fft.o fftFunctions.o addfunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking_localhom',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2062:3:
Salignmm.c:469:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  469 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking_localhom',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2062:3:
Salignmm.c:471:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  471 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
gcc -o maffttext2hex maffttext2hex.c  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
maffttext2hex.c: In function 'main':
maffttext2hex.c:55:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
   55 |                         fgets( (char *)buf, 999, fp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -o hex2maffttext hex2maffttext.c  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c splittbfast.c
splittbfast.c: In function 'callfasta':
splittbfast.c:317:20: warning: variable 'ninbk' set but not used [-Wunused-but-set-variable]
  317 |         static int ninbk = 0;
      |                    ^~~~~
splittbfast.c:316:24: warning: variable 'scoresbk' set but not used [-Wunused-but-set-variable]
  316 |         static Scores *scoresbk = NULL;
      |                        ^~~~~~~~
splittbfast.c: In function 'pairalign':
splittbfast.c:953:24: warning: variable 'tscore' set but not used [-Wunused-but-set-variable]
  953 |         double pscore, tscore;
      |                        ^~~~~~
splittbfast.c:953:16: warning: variable 'pscore' set but not used [-Wunused-but-set-variable]
  953 |         double pscore, tscore;
      |                ^~~~~~
splittbfast.c: In function 'splitseq_mq':
splittbfast.c:1491:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
 1491 |         for( i=0; i<nin; i++ ) pickkouho[i] = i+1; nkouho = nin-1; // zenbu
      |         ^~~
splittbfast.c:1491:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
 1491 |         for( i=0; i<nin; i++ ) pickkouho[i] = i+1; nkouho = nin-1; // zenbu
      |                                                    ^~~~~~
splittbfast.c: In function 'main':
splittbfast.c:2696:13: warning: variable 'completed' set but not used [-Wunused-but-set-variable]
 2696 |         int completed;
      |             ^~~~~~~~~
splittbfast.c:3236:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 3236 |                 system( com );
      |                 ^~~~~~~~~~~~~
gcc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o  Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o splittbfast.o defs.o fft.o fftFunctions.o   -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c disttbfast.c
disttbfast.c: In function 'checkanchors_strongestfirst_considerseparation':
disttbfast.c:1512:51: warning: operation on '(a + (sizetype)((long unsigned int)p * 28))->startj' may be undefined [-Wsequence-point]
 1512 |                         a[p].starti = a[p].startj = a[p].startj = a[p].endj = -1;
      |                                       ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
disttbfast.c:1552:59: warning: operation on '(a + (sizetype)((long unsigned int)q * 28))->startj' may be undefined [-Wsequence-point]
 1552 |                                 a[q].starti = a[q].startj = a[q].startj = a[q].endj = -1;
      |                                               ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
disttbfast.c: In function 'checkanchors_strongestfirst':
disttbfast.c:1613:59: warning: operation on '(a + (sizetype)((long unsigned int)q * 28))->startj' may be undefined [-Wsequence-point]
 1613 |                                 a[q].starti = a[q].startj = a[q].startj = a[q].endj = -1;
      |                                               ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
disttbfast.c: In function 'dooneiteration':
disttbfast.c:2650:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2650 |         if( effarr1 ) free( effarr1 ); effarr1 = NULL;
      |         ^~
disttbfast.c:2650:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2650 |         if( effarr1 ) free( effarr1 ); effarr1 = NULL;
      |                                        ^~~~~~~
disttbfast.c:2651:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2651 |         if( effarr2 ) free( effarr2 ); effarr2 = NULL;
      |         ^~
disttbfast.c:2651:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2651 |         if( effarr2 ) free( effarr2 ); effarr2 = NULL;
      |                                        ^~~~~~~
disttbfast.c:2652:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2652 |         if( indication1 ) free( indication1 ); indication1 = NULL;
      |         ^~
disttbfast.c:2652:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2652 |         if( indication1 ) free( indication1 ); indication1 = NULL;
      |                                                ^~~~~~~~~~~
disttbfast.c:2653:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2653 |         if( indication2 ) free( indication2 ); indication2 = NULL;
      |         ^~
disttbfast.c:2653:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2653 |         if( indication2 ) free( indication2 ); indication2 = NULL;
      |                                                ^~~~~~~~~~~
disttbfast.c:2654:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2654 |         if( fftlog ) free( fftlog ); fftlog = NULL;
      |         ^~
disttbfast.c:2654:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2654 |         if( fftlog ) free( fftlog ); fftlog = NULL;
      |                                      ^~~~~~
disttbfast.c:2655:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2655 |         if( alreadyaligned ) free( alreadyaligned ); alreadyaligned = NULL;
      |         ^~
disttbfast.c:2655:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2655 |         if( alreadyaligned ) free( alreadyaligned ); alreadyaligned = NULL;
      |                                                      ^~~~~~~~~~~~~~
disttbfast.c:2658:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2658 |                 if( dynamicmtx ) FreeDoubleMtx( dynamicmtx ); dynamicmtx = NULL;
      |                 ^~
disttbfast.c:2658:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2658 |                 if( dynamicmtx ) FreeDoubleMtx( dynamicmtx ); dynamicmtx = NULL;
      |                                                               ^~~~~~~~~~
disttbfast.c:2660:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2660 |         if( localmem ) free( localmem ); localmem = NULL;
      |         ^~
disttbfast.c:2660:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2660 |         if( localmem ) free( localmem ); localmem = NULL;
      |                                          ^~~~~~~~
disttbfast.c:2662:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2662 |         if( skiptable1 ) FreeIntMtx( skiptable1 ); skiptable1 = NULL;
      |         ^~
disttbfast.c:2662:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2662 |         if( skiptable1 ) FreeIntMtx( skiptable1 ); skiptable1 = NULL;
      |                                                    ^~~~~~~~~~
disttbfast.c:2663:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2663 |         if( skiptable2 ) FreeIntMtx( skiptable2 ); skiptable2 = NULL;
      |         ^~
disttbfast.c:2663:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2663 |         if( skiptable2 ) FreeIntMtx( skiptable2 ); skiptable2 = NULL;
      |                                                    ^~~~~~~~~~
disttbfast.c:2350:16: warning: variable 'pscore' set but not used [-Wunused-but-set-variable]
 2350 |         double pscore;
      |                ^~~~~~
disttbfast.c: In function 'treebase':
disttbfast.c:3229:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3229 |         if( effarr1 ) free( effarr1 ); effarr1 = NULL;
      |         ^~
disttbfast.c:3229:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3229 |         if( effarr1 ) free( effarr1 ); effarr1 = NULL;
      |                                        ^~~~~~~
disttbfast.c:3230:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3230 |         if( effarr2 ) free( effarr2 ); effarr2 = NULL;
      |         ^~
disttbfast.c:3230:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3230 |         if( effarr2 ) free( effarr2 ); effarr2 = NULL;
      |                                        ^~~~~~~
disttbfast.c:3231:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3231 |         if( indication1 ) free( indication1 ); indication1 = NULL;
      |         ^~
disttbfast.c:3231:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3231 |         if( indication1 ) free( indication1 ); indication1 = NULL;
      |                                                ^~~~~~~~~~~
disttbfast.c:3232:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3232 |         if( indication2 ) free( indication2 ); indication2 = NULL;
      |         ^~
disttbfast.c:3232:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3232 |         if( indication2 ) free( indication2 ); indication2 = NULL;
      |                                                ^~~~~~~~~~~
disttbfast.c:3233:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3233 |         if( fftlog ) free( fftlog ); fftlog = NULL;
      |         ^~
disttbfast.c:3233:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3233 |         if( fftlog ) free( fftlog ); fftlog = NULL;
      |                                      ^~~~~~
disttbfast.c:3234:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3234 |         if( gaplen ) free( gaplen ); gaplen = NULL;
      |         ^~
disttbfast.c:3234:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3234 |         if( gaplen ) free( gaplen ); gaplen = NULL;
      |                                      ^~~~~~
disttbfast.c:3235:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3235 |         if( gapmap ) free( gapmap ); gapmap = NULL;
      |         ^~
disttbfast.c:3235:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3235 |         if( gapmap ) free( gapmap ); gapmap = NULL;
      |                                      ^~~~~~
disttbfast.c:3236:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3236 |         if( alreadyaligned ) free( alreadyaligned ); alreadyaligned = NULL;
      |         ^~
disttbfast.c:3236:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3236 |         if( alreadyaligned ) free( alreadyaligned ); alreadyaligned = NULL;
      |                                                      ^~~~~~~~~~~~~~
disttbfast.c:3239:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3239 |                 if( dynamicmtx ) FreeDoubleMtx( dynamicmtx ); dynamicmtx = NULL;
      |                 ^~
disttbfast.c:3239:63: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3239 |                 if( dynamicmtx ) FreeDoubleMtx( dynamicmtx ); dynamicmtx = NULL;
      |                                                               ^~~~~~~~~~
disttbfast.c:3241:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3241 |         if( localmem ) free( localmem ); localmem = NULL;
      |         ^~
disttbfast.c:3241:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3241 |         if( localmem ) free( localmem ); localmem = NULL;
      |                                          ^~~~~~~~
disttbfast.c:3243:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3243 |         if( skiptable1 ) FreeIntMtx( skiptable1 ); skiptable1 = NULL;
      |         ^~
disttbfast.c:3243:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3243 |         if( skiptable1 ) FreeIntMtx( skiptable1 ); skiptable1 = NULL;
      |                                                    ^~~~~~~~~~
disttbfast.c:3244:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3244 |         if( skiptable2 ) FreeIntMtx( skiptable2 ); skiptable2 = NULL;
      |         ^~
disttbfast.c:3244:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3244 |         if( skiptable2 ) FreeIntMtx( skiptable2 ); skiptable2 = NULL;
      |                                                    ^~~~~~~~~~
disttbfast.c:2671:30: warning: variable 'len2nocommongap' set but not used [-Wunused-but-set-variable]
 2671 |         int len1nocommongap, len2nocommongap;
      |                              ^~~~~~~~~~~~~~~
disttbfast.c: In function 'disttbfast':
disttbfast.c:4151:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4151 |                                 if( mindistfrom ) free( mindistfrom ); mindistfrom = NULL;
      |                                 ^~
disttbfast.c:4151:72: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4151 |                                 if( mindistfrom ) free( mindistfrom ); mindistfrom = NULL;
      |                                                                        ^~~~~~~~~~~
disttbfast.c:4153:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4153 |                                 if( selfscore ) free( selfscore ); selfscore = NULL;
      |                                 ^~
disttbfast.c:4153:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4153 |                                 if( selfscore ) free( selfscore ); selfscore = NULL;
      |                                                                    ^~~~~~~~~
disttbfast.c:4154:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4154 |                                 if( bseq ) FreeCharMtx( bseq ); bseq = NULL; // nikaime dake
      |                                 ^~
disttbfast.c:4154:65: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4154 |                                 if( bseq ) FreeCharMtx( bseq ); bseq = NULL; // nikaime dake
      |                                                                 ^~~~
disttbfast.c:4155:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4155 |                                 if( skiptable) FreeIntMtx( skiptable ); skiptable = NULL; // nikaime dake
      |                                 ^~
disttbfast.c:4155:73: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4155 |                                 if( skiptable) FreeIntMtx( skiptable ); skiptable = NULL; // nikaime dake
      |                                                                         ^~~~~~~~~
disttbfast.c:4156:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4156 |                                 if( pointt ) FreeIntMtx( pointt ); pointt = NULL; // ikkaime dake.
      |                                 ^~
disttbfast.c:4156:68: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4156 |                                 if( pointt ) FreeIntMtx( pointt ); pointt = NULL; // ikkaime dake.
      |                                                                    ^~~~~~
disttbfast.c:4824:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 4824 |                         if( skiptable) FreeIntMtx( skiptable ); skiptable = NULL;
      |                         ^~
disttbfast.c:4824:65: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 4824 |                         if( skiptable) FreeIntMtx( skiptable ); skiptable = NULL;
      |                                                                 ^~~~~~~~~
disttbfast.c:5106:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5106 |         if( originalgaps ) free( originalgaps ); originalgaps = NULL;
      |         ^~
disttbfast.c:5106:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5106 |         if( originalgaps ) free( originalgaps ); originalgaps = NULL;
      |                                                  ^~~~~~~~~~~~
disttbfast.c:5120:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5120 |         if( nlen ) free( nlen ); nlen = NULL;
      |         ^~
disttbfast.c:5120:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5120 |         if( nlen ) free( nlen ); nlen = NULL;
      |                                  ^~~~
disttbfast.c:5121:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5121 |         if( seq ) FreeCharMtx( seq ); seq = NULL;
      |         ^~
disttbfast.c:5121:39: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5121 |         if( seq ) FreeCharMtx( seq ); seq = NULL;
      |                                       ^~~
disttbfast.c:5122:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5122 |         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |         ^~
disttbfast.c:5122:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5122 |         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                                    ^~~~~
disttbfast.c:5123:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5123 |         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |         ^~
disttbfast.c:5123:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5123 |         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                                    ^~~~~
disttbfast.c:5140:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5140 |         if( topol ) FreeIntCub( topol ); topol = NULL;
      |         ^~
disttbfast.c:5140:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5140 |         if( topol ) FreeIntCub( topol ); topol = NULL;
      |                                          ^~~~~
disttbfast.c:5141:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5141 |         if( len ) FreeFloatMtx( len ); len = NULL;
      |         ^~
disttbfast.c:5141:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5141 |         if( len ) FreeFloatMtx( len ); len = NULL;
      |                                        ^~~
disttbfast.c:5142:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5142 |         if( eff ) free( eff ); eff = NULL;
      |         ^~
disttbfast.c:5142:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5142 |         if( eff ) free( eff ); eff = NULL;
      |                                ^~~
disttbfast.c:5143:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5143 |         if( mergeoralign ) free( mergeoralign ); mergeoralign = NULL;
      |         ^~
disttbfast.c:5143:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5143 |         if( mergeoralign ) free( mergeoralign ); mergeoralign = NULL;
      |                                                  ^~~~~~~~~~~~
disttbfast.c:5144:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5144 |         if( dep ) free( dep ); dep = NULL;
      |         ^~
disttbfast.c:5144:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5144 |         if( dep ) free( dep ); dep = NULL;
      |                                ^~~
disttbfast.c:5145:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5145 |         if( addmem ) free( addmem ); addmem = NULL;
      |         ^~
disttbfast.c:5145:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5145 |         if( addmem ) free( addmem ); addmem = NULL;
      |                                      ^~~~~~
disttbfast.c:5146:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5146 |         if( localmem ) FreeIntMtx( localmem ); localmem = NULL;
      |         ^~
disttbfast.c:5146:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5146 |         if( localmem ) FreeIntMtx( localmem ); localmem = NULL;
      |                                                ^~~~~~~~
disttbfast.c:5147:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5147 |         if( name ) FreeCharMtx( name ); name = NULL;
      |         ^~
disttbfast.c:5147:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5147 |         if( name ) FreeCharMtx( name ); name = NULL;
      |                                         ^~~~
disttbfast.c:5148:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5148 |         if( nogaplen ) free( nogaplen ); nogaplen = NULL;
      |         ^~
disttbfast.c:5148:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5148 |         if( nogaplen ) free( nogaplen ); nogaplen = NULL;
      |                                          ^~~~~~~~
disttbfast.c:5150:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5150 |         if( tmpseq ) free( tmpseq ); tmpseq = NULL;
      |         ^~
disttbfast.c:5150:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5150 |         if( tmpseq ) free( tmpseq ); tmpseq = NULL;
      |                                      ^~~~~~
disttbfast.c:5151:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5151 |         if( grpseq ) free( grpseq ); grpseq = NULL;
      |         ^~
disttbfast.c:5151:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5151 |         if( grpseq ) free( grpseq ); grpseq = NULL;
      |                                      ^~~~~~
disttbfast.c:5152:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5152 |         if( pointt ) FreeIntMtx( pointt ); pointt = NULL;
      |         ^~
disttbfast.c:5152:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5152 |         if( pointt ) FreeIntMtx( pointt ); pointt = NULL;
      |                                            ^~~~~~
disttbfast.c:5153:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5153 |         if( mtx ) FreeFloatHalfMtx( mtx, njob ); mtx = NULL;
      |         ^~
disttbfast.c:5153:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5153 |         if( mtx ) FreeFloatHalfMtx( mtx, njob ); mtx = NULL;
      |                                                  ^~~
disttbfast.c:5154:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5154 |         if( table1 ) free( table1 ); table1 = NULL;
      |         ^~
disttbfast.c:5154:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5154 |         if( table1 ) free( table1 ); table1 = NULL;
      |                                      ^~~~~~
disttbfast.c:5156:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5156 |         if( bseq ) FreeCharMtx( bseq ); bseq = NULL;
      |         ^~
disttbfast.c:5156:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5156 |         if( bseq ) FreeCharMtx( bseq ); bseq = NULL;
      |                                         ^~~~
disttbfast.c:5157:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5157 |         if( selfscore ) free( selfscore ); selfscore = NULL;
      |         ^~
disttbfast.c:5157:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5157 |         if( selfscore ) free( selfscore ); selfscore = NULL;
      |                                            ^~~~~~~~~
disttbfast.c:5158:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5158 |         if( skiptable ) FreeIntMtx( skiptable ); skiptable = NULL;
      |         ^~
disttbfast.c:5158:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5158 |         if( skiptable ) FreeIntMtx( skiptable ); skiptable = NULL;
      |                                                  ^~~~~~~~~
disttbfast.c:5159:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5159 |         if( originalgaps ) free( originalgaps ); originalgaps = NULL;
      |         ^~
disttbfast.c:5159:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5159 |         if( originalgaps ) free( originalgaps ); originalgaps = NULL;
      |                                                  ^~~~~~~~~~~~
disttbfast.c:5168:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5168 |         if( subtable ) FreeIntMtx( subtable ); subtable = NULL;
      |         ^~
disttbfast.c:5168:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5168 |         if( subtable ) FreeIntMtx( subtable ); subtable = NULL;
      |                                                ^~~~~~~~
disttbfast.c:5169:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5169 |         if( insubtable ) free( insubtable ); insubtable = NULL;
      |         ^~
disttbfast.c:5169:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5169 |         if( insubtable ) free( insubtable ); insubtable = NULL;
      |                                              ^~~~~~~~~~
disttbfast.c:5172:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5172 |                 if( subalnpt[i] ) free( subalnpt[i] ); subalnpt[i] = NULL;
      |                 ^~
disttbfast.c:5172:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5172 |                 if( subalnpt[i] ) free( subalnpt[i] ); subalnpt[i] = NULL;
      |                                                        ^~~~~~~~
disttbfast.c:5174:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5174 |         if( subalnpt ) free( subalnpt ); subalnpt = NULL;
      |         ^~
disttbfast.c:5174:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5174 |         if( subalnpt ) free( subalnpt ); subalnpt = NULL;
      |                                          ^~~~~~~~
disttbfast.c:5175:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5175 |         if( preservegaps ) free( preservegaps ); preservegaps = NULL;
      |         ^~
disttbfast.c:5175:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5175 |         if( preservegaps ) free( preservegaps ); preservegaps = NULL;
      |                                                  ^~~~~~~~~~~~
disttbfast.c:5178:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5178 |         if( mindistfrom ) free( mindistfrom ); mindistfrom = NULL;
      |         ^~
disttbfast.c:5178:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5178 |         if( mindistfrom ) free( mindistfrom ); mindistfrom = NULL;
      |                                                ^~~~~~~~~~~
disttbfast.c:5179:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5179 |         if( mindist ) free( mindist ); mindist = NULL;
      |         ^~
disttbfast.c:5179:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5179 |         if( mindist ) free( mindist ); mindist = NULL;
      |                                        ^~~~~~~
disttbfast.c:5185:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5185 |                         if( cpmxhist[i] ) FreeDoubleMtx( cpmxhist[i] ); cpmxhist[i] = NULL;
      |                         ^~
disttbfast.c:5185:73: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5185 |                         if( cpmxhist[i] ) FreeDoubleMtx( cpmxhist[i] ); cpmxhist[i] = NULL;
      |                                                                         ^~~~~~~~
disttbfast.c:5194:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 5194 |                         if( memhist[i] ) free( memhist[i] ); memhist[i] = NULL;
      |                         ^~
disttbfast.c:5194:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 5194 |                         if( memhist[i] ) free( memhist[i] ); memhist[i] = NULL;
      |                                                              ^~~~~~~
disttbfast.c:3412:13: warning: variable 'posinmem' set but not used [-Wunused-but-set-variable]
 3412 |         int posinmem;
      |             ^~~~~~~~
disttbfast.c:4517:41: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 4517 |                                         system( "cp infile.tree GuideTree" ); // tekitou
      |                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'checkanchors_strongestfirst_considerseparation',
    inlined from 'pickpairanch' at disttbfast.c:1814:3:
disttbfast.c:1495:30: warning: 'nearest' may be used uninitialized [-Wmaybe-uninitialized]
 1495 |                         if( a[nearest].starti < a[p].starti )
      |                              ^
disttbfast.c: In function 'pickpairanch':
disttbfast.c:1480:21: note: 'nearest' was declared here
 1480 |                 int nearest, mindist;
      |                     ^~~~~~~
disttbfast.c: In function 'treebasethread':
disttbfast.c:1933:33: warning: 'dynamicmtx' may be used uninitialized [-Wmaybe-uninitialized]
 1933 |                                 FreeDoubleMtx( dynamicmtx );
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~
disttbfast.c:1865:18: note: 'dynamicmtx' was declared here
 1865 |         double **dynamicmtx;
      |                  ^~~~~~~~~~
gcc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
mltaln9.c: In function 'fixed_musclesupg_double_realloc_nobk_halfmtx_treeout_memsave.isra':
mltaln9.c:6494:28: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 6494 |                 int *mem = calloc( sizeof( int ), nseq );
      |                            ^
/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'fgets',
    inlined from 'check_guidetreefile' at mltaln9.c:2850:2,
    inlined from 'disttbfast.constprop' at disttbfast.c:3623:12:
/usr/include/bits/stdio2.h:215:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  215 |     return __fgets_chk_warn (__s, sz, __n, __stream);
      |            ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c tbfast.c
tbfast.c: In function 'treebasethread':
tbfast.c:815:13: warning: variable 'posinmem' set but not used [-Wunused-but-set-variable]
  815 |         int posinmem;
      |             ^~~~~~~~
tbfast.c:800:16: warning: variable 'pscore' set but not used [-Wunused-but-set-variable]
  800 |         double pscore;
      |                ^~~~~~
tbfast.c: In function 'treebase':
tbfast.c:1252:13: warning: unused variable 'posinmem' [-Wunused-variable]
 1252 |         int posinmem;
      |             ^~~~~~~~
tbfast.c:1227:30: warning: variable 'len2nocommongap' set but not used [-Wunused-but-set-variable]
 1227 |         int len1nocommongap, len2nocommongap;
      |                              ^~~~~~~~~~~~~~~
tbfast.c: In function 'preparepartmtx':
tbfast.c:1869:16: warning: variable 'size' set but not used [-Wunused-but-set-variable]
 1869 |         double size;
      |                ^~~~
tbfast.c: In function 'main':
tbfast.c:2174:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2174 |                         if( expdist ) FreeDoubleMtx( expdist ); expdist = NULL;
      |                         ^~
tbfast.c:2174:65: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2174 |                         if( expdist ) FreeDoubleMtx( expdist ); expdist = NULL;
      |                                                                 ^~~~~~~
tbfast.c:2329:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2329 |                         if( expdist ) FreeDoubleMtx( expdist ); expdist = NULL;
      |                         ^~
tbfast.c:2329:65: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2329 |                         if( expdist ) FreeDoubleMtx( expdist ); expdist = NULL;
      |                                                                 ^~~~~~~
tbfast.c:2890:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2890 |                         if( mindistfrom ) free( mindistfrom ); mindistfrom = NULL;
      |                         ^~
tbfast.c:2890:64: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2890 |                         if( mindistfrom ) free( mindistfrom ); mindistfrom = NULL;
      |                                                                ^~~~~~~~~~~
tbfast.c:2893:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2893 |                         if( skiptable) FreeIntMtx( skiptable ); skiptable = NULL; // nikaime dake
      |                         ^~
tbfast.c:2893:65: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2893 |                         if( skiptable) FreeIntMtx( skiptable ); skiptable = NULL; // nikaime dake
      |                                                                 ^~~~~~~~~
tbfast.c:3008:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3008 |         if( iscore ) FreeFloatHalfMtx( iscore, njob ); iscore = NULL;
      |         ^~
tbfast.c:3008:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3008 |         if( iscore ) FreeFloatHalfMtx( iscore, njob ); iscore = NULL;
      |                                                        ^~~~~~
tbfast.c:3009:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3009 |         if( iscore_kozo ) FreeFloatHalfMtx( iscore_kozo, nkozo ); iscore = NULL;
      |         ^~
tbfast.c:3009:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3009 |         if( iscore_kozo ) FreeFloatHalfMtx( iscore_kozo, nkozo ); iscore = NULL;
      |                                                                   ^~~~~~
tbfast.c:3010:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3010 |         if( topol_kozo ) FreeIntCub( topol_kozo ); topol_kozo = NULL;
      |         ^~
tbfast.c:3010:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3010 |         if( topol_kozo ) FreeIntCub( topol_kozo ); topol_kozo = NULL;
      |                                                    ^~~~~~~~~~
tbfast.c:3011:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3011 |         if( len_kozo ) FreeFloatMtx( len_kozo ); len_kozo = NULL;
      |         ^~
tbfast.c:3011:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3011 |         if( len_kozo ) FreeFloatMtx( len_kozo ); len_kozo = NULL;
      |                                                  ^~~~~~~~
tbfast.c:3012:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3012 |         if( eff_kozo ) free( eff_kozo ); eff_kozo = NULL;
      |         ^~
tbfast.c:3012:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3012 |         if( eff_kozo ) free( eff_kozo ); eff_kozo = NULL;
      |                                          ^~~~~~~~
tbfast.c:3565:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3565 |         if( constraint && compacttree == 3 && uselh ) free( uselh ); uselh = NULL;
      |         ^~
tbfast.c:3565:70: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3565 |         if( constraint && compacttree == 3 && uselh ) free( uselh ); uselh = NULL;
      |                                                                      ^~~~~
tbfast.c:3602:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3602 |         if( nfilesfornode ) free( nfilesfornode ); nfilesfornode = NULL;
      |         ^~
tbfast.c:3602:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3602 |         if( nfilesfornode ) free( nfilesfornode ); nfilesfornode = NULL;
      |                                                    ^~~~~~~~~~~~~
tbfast.c:3606:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3606 |         if( eff_kozo_mapped ) free( eff_kozo_mapped ); eff_kozo_mapped = NULL;
      |         ^~
tbfast.c:3606:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3606 |         if( eff_kozo_mapped ) free( eff_kozo_mapped ); eff_kozo_mapped = NULL;
      |                                                        ^~~~~~~~~~~~~~~
tbfast.c:3611:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3611 |         if( seq ) FreeCharMtx( seq ); seq = NULL;
      |         ^~
tbfast.c:3611:39: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3611 |         if( seq ) FreeCharMtx( seq ); seq = NULL;
      |                                       ^~~
tbfast.c:3612:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3612 |         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |         ^~
tbfast.c:3612:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3612 |         if( mseq1 ) free( mseq1 ); mseq1 = NULL;
      |                                    ^~~~~
tbfast.c:3613:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3613 |         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |         ^~
tbfast.c:3613:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3613 |         if( mseq2 ) free( mseq2 ); mseq2 = NULL;
      |                                    ^~~~~
tbfast.c:3615:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3615 |         if( name ) FreeCharMtx( name ); name = NULL;
      |         ^~
tbfast.c:3615:41: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3615 |         if( name ) FreeCharMtx( name ); name = NULL;
      |                                         ^~~~
tbfast.c:3616:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3616 |         if( nlen ) free( nlen ); nlen = NULL;
      |         ^~
tbfast.c:3616:34: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3616 |         if( nlen ) free( nlen ); nlen = NULL;
      |                                  ^~~~
tbfast.c:3617:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3617 |         if( selfscore ) free( selfscore ); selfscore = NULL;
      |         ^~
tbfast.c:3617:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3617 |         if( selfscore ) free( selfscore ); selfscore = NULL;
      |                                            ^~~~~~~~~
tbfast.c:3618:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3618 |         if( mergeoralign ) free( mergeoralign ); mergeoralign = NULL;
      |         ^~
tbfast.c:3618:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3618 |         if( mergeoralign ) free( mergeoralign ); mergeoralign = NULL;
      |                                                  ^~~~~~~~~~~~
tbfast.c:3629:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3629 |         if( targetmap ) free( targetmap ); targetmap = NULL;
      |         ^~
tbfast.c:3629:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3629 |         if( targetmap ) free( targetmap ); targetmap = NULL;
      |                                            ^~~~~~~~~
tbfast.c:3630:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3630 |         if( targetmapr ) free( targetmapr ); targetmapr = NULL;
      |         ^~
tbfast.c:3630:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3630 |         if( targetmapr ) free( targetmapr ); targetmapr = NULL;
      |                                              ^~~~~~~~~~
tbfast.c:3631:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3631 |         if( uselh ) free( uselh ); uselh = NULL;
      |         ^~
tbfast.c:3631:36: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3631 |         if( uselh ) free( uselh ); uselh = NULL;
      |                                    ^~~~~
tbfast.c:3633:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3633 |         if( kozoarivec ) free( kozoarivec ); kozoarivec = NULL;
      |         ^~
tbfast.c:3633:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3633 |         if( kozoarivec ) free( kozoarivec ); kozoarivec = NULL;
      |                                              ^~~~~~~~~~
tbfast.c:3634:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3634 |         if( eff_kozo_mapped ) free( eff_kozo_mapped ); eff_kozo_mapped = NULL;
      |         ^~
tbfast.c:3634:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3634 |         if( eff_kozo_mapped ) free( eff_kozo_mapped ); eff_kozo_mapped = NULL;
      |                                                        ^~~~~~~~~~~~~~~
tbfast.c:3635:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3635 |         if( eff_kozo ) free( eff_kozo ); eff_kozo = NULL;
      |         ^~
tbfast.c:3635:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3635 |         if( eff_kozo ) free( eff_kozo ); eff_kozo = NULL;
      |                                          ^~~~~~~~
tbfast.c:3638:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3638 |         if( topol ) FreeIntCub( topol ); topol = NULL;
      |         ^~
tbfast.c:3638:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3638 |         if( topol ) FreeIntCub( topol ); topol = NULL;
      |                                          ^~~~~
tbfast.c:3639:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3639 |         if( topol_kozo ) FreeIntCub( topol_kozo ); topol_kozo = NULL;
      |         ^~
tbfast.c:3639:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3639 |         if( topol_kozo ) FreeIntCub( topol_kozo ); topol_kozo = NULL;
      |                                                    ^~~~~~~~~~
tbfast.c:3640:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3640 |         if( len ) FreeFloatMtx( len ); len = NULL;
      |         ^~
tbfast.c:3640:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3640 |         if( len ) FreeFloatMtx( len ); len = NULL;
      |                                        ^~~
tbfast.c:3641:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3641 |         if( len_kozo ) FreeFloatMtx( len_kozo ); len_kozo = NULL;
      |         ^~
tbfast.c:3641:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3641 |         if( len_kozo ) FreeFloatMtx( len_kozo ); len_kozo = NULL;
      |                                                  ^~~~~~~~
tbfast.c:3642:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3642 |         if( iscore ) FreeFloatHalfMtx( iscore, njob ); iscore = NULL;
      |         ^~
tbfast.c:3642:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3642 |         if( iscore ) FreeFloatHalfMtx( iscore, njob ); iscore = NULL;
      |                                                        ^~~~~~
tbfast.c:3643:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3643 |         if( iscore_kozo && nseed ) FreeFloatHalfMtx( iscore_kozo, nseed ); iscore = NULL; // ? nseed?
      |         ^~
tbfast.c:3643:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3643 |         if( iscore_kozo && nseed ) FreeFloatHalfMtx( iscore_kozo, nseed ); iscore = NULL; // ? nseed?
      |                                                                            ^~~~~~
tbfast.c:3644:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3644 |         if( eff ) free( eff ); eff = NULL;
      |         ^~
tbfast.c:3644:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3644 |         if( eff ) free( eff ); eff = NULL;
      |                                ^~~
tbfast.c:3645:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3645 |         if( dep ) free( dep ); dep = NULL;
      |         ^~
tbfast.c:3645:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3645 |         if( dep ) free( dep ); dep = NULL;
      |                                ^~~
tbfast.c:3646:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3646 |         if( nfilesfornode ) free( nfilesfornode ); nfilesfornode = NULL;
      |         ^~
tbfast.c:3646:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3646 |         if( nfilesfornode ) free( nfilesfornode ); nfilesfornode = NULL;
      |                                                    ^~~~~~~~~~~~~
tbfast.c:3648:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3648 |         if( addmem ) free( addmem ); addmem = NULL;
      |         ^~
tbfast.c:3648:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3648 |         if( addmem ) free( addmem ); addmem = NULL;
      |                                      ^~~~~~
tbfast.c:3649:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 3649 |         if( localmem ) FreeIntMtx( localmem ); localmem = NULL;
      |         ^~
tbfast.c:3649:48: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 3649 |         if( localmem ) FreeIntMtx( localmem ); localmem = NULL;
      |                                                ^~~~~~~~
tbfast.c:1916:13: warning: variable 'posinmem' set but not used [-Wunused-but-set-variable]
 1916 |         int posinmem;
      |             ^~~~~~~~
tbfast.c:3254:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
 3254 |                                 system( "cp infile.tree GuideTree" ); // tekitou
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tbfast.c:2864:25: warning: 'subtable' may be used uninitialized [-Wmaybe-uninitialized]
 2864 |                         fixed_supg_double_realloc_nobk_halfmtx_treeout_constrained( njob, iscore, topol, len, name, nlen, dep, nsubalignments, subtable, 1 );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tbfast.c:1907:15: note: 'subtable' was declared here
 1907 |         int **subtable;
      |               ^~~~~~~~
tbfast.c:3233:43: warning: 'insubtable' may be used uninitialized [-Wmaybe-uninitialized]
 3233 |                                 insubtable[subtable[i][j]] = 1;
      |                                           ^
tbfast.c:1908:14: note: 'insubtable' was declared here
 1908 |         int *insubtable;
      |              ^~~~~~~~~~
tbfast.c:3309:17: warning: 'preservegaps' may be used uninitialized [-Wmaybe-uninitialized]
 3309 |                 free( preservegaps );
      |                 ^~~~~~~~~~~~~~~~~~~~
tbfast.c:1909:14: note: 'preservegaps' was declared here
 1909 |         int *preservegaps;
      |              ^~~~~~~~~~~~
tbfast.c:3308:17: warning: 'subalnpt' may be used uninitialized [-Wmaybe-uninitialized]
 3308 |                 free( subalnpt );
      |                 ^~~~~~~~~~~~~~~~
tbfast.c:1910:17: note: 'subalnpt' was declared here
 1910 |         char ***subalnpt;
      |                 ^~~~~~~~
tbfast.c:3434:9: warning: 'ntarget' may be used uninitialized [-Wmaybe-uninitialized]
 3434 |         treebase( nlen, bseq, nadd, mergeoralign, mseq1, mseq2, topol, dep, eff, &alloclen, localhomtable, singlerna, eff_kozo_mapped, targetmap, targetmapr, ntarget, uselh, nseed, nfilesfornode );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tbfast.c:1932:13: note: 'ntarget' was declared here
 1932 |         int ntarget;
      |             ^~~~~~~
tbfast.c:2887:25: warning: 'skiptable' may be used uninitialized [-Wmaybe-uninitialized]
 2887 |                         compacttree_memsaveselectable( njob, partmtx, mindistfrom, mindist, NULL, selfscore, seq, skiptable, topol, len, name, NULL, dep, treeout, compacttree, 1 );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tbfast.c:1890:15: note: 'skiptable' was declared here
 1890 |         int **skiptable;
      |               ^~~~~~~~~
gcc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o tbfast.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o   -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
In function 'fgets',
    inlined from 'check_guidetreefile' at mltaln9.c:2850:2:
/usr/include/bits/stdio2.h:215:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  215 |     return __fgets_chk_warn (__s, sz, __n, __stream);
      |            ^
In function 'Atracking',
    inlined from 'A__align.constprop' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking_localhom',
    inlined from 'A__align.constprop' at Salignmm.c:2062:3:
Salignmm.c:469:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  469 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking_localhom',
    inlined from 'A__align.constprop' at Salignmm.c:2062:3:
Salignmm.c:471:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  471 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
mltaln9.c: In function 'fixed_musclesupg_double_realloc_nobk_halfmtx_treeout_memsave.constprop':
mltaln9.c:6494:28: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 6494 |                 int *mem = calloc( sizeof( int ), nseq );
      |                            ^
/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here
  675 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c nodepair.c
gcc -o nodepair mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o nodepair.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c mafft-profile.c
mafft-profile.c: In function 'GroupAlign':
mafft-profile.c:190:17: warning: variable 's2' set but not used [-Wunused-but-set-variable]
  190 |         int s1, s2;
      |                 ^~
mafft-profile.c:190:13: warning: variable 's1' set but not used [-Wunused-but-set-variable]
  190 |         int s1, s2;
      |             ^~
mafft-profile.c: In function 'main':
mafft-profile.c:321:23: warning: variable 'bseq' set but not used [-Wunused-but-set-variable]
  321 |         static char **bseq;
      |                       ^~~~
gcc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o SAalignmm.o Galign11.o Lalign11.o genalign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
In function 'Atracking',
    inlined from 'A__align.constprop' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c f2cl.c
f2cl.c: In function 'main':
f2cl.c:297:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  297 |                         fgets( gett, B-1, orderfp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c mccaskillwrap.c
mccaskillwrap.c: In function 'main':
mccaskillwrap.c:372:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  372 |                         system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mccaskillwrap.c: In function 'athread':
mccaskillwrap.c:115:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  115 |                 system( com );
      |                 ^~~~~~~~~~~~~
mccaskillwrap.c:117:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  117 |                 system( com );
      |                 ^~~~~~~~~~~~~
mccaskillwrap.c:129:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  129 |                 system( com ); // for cygwin, wakaran
      |                 ^~~~~~~~~~~~~
mccaskillwrap.c:155:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result]
  155 |                         system( com );
      |                         ^~~~~~~~~~~~~
mccaskillwrap.c: In function 'readrawmccaskill':
mccaskillwrap.c:46:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
   46 |                 fgets( gett, 999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~
gcc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c contrafoldwrap.c
contrafoldwrap.c: In function 'readcontrafold':
contrafoldwrap.c:57:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
   57 |                 fgets( gett, 9999, fp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~
gcc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c countlen.c
gcc -o countlen mtxutl.o io.o countlen.o defs.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c seq2regtable.c
seq2regtable.c: In function 'main':
seq2regtable.c:79:17: warning: 'weboutfp' may be used uninitialized [-Wmaybe-uninitialized]
   79 |                 getnumlen_nogap_outallreg_web( infp, weboutfp, &nlenmin, &isaligned );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seq2regtable.c:48:15: note: 'weboutfp' was declared here
   48 |         FILE *weboutfp;
      |               ^~~~~~~~
gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c regtable2seq.c
regtable2seq.c: In function 'readereg':
regtable2seq.c:69:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
   69 |         fgets( gett, 999, regfp );
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~
regtable2seq.c:97:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
   97 |                 fgets( gett, 999, regfp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~
regtable2seq.c: In function 'readreg':
regtable2seq.c:120:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  120 |                 fgets( gett, 999, regfp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c score.c
gcc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c getlag.c
getlag.c: In function 'treebase':
getlag.c:168:25: warning: variable 'partialeff' set but not used [-Wunused-but-set-variable]
  168 |         static double **partialeff = NULL;
      |                         ^~~~~~~~~~
getlag.c:167:25: warning: variable 'partiallen' set but not used [-Wunused-but-set-variable]
  167 |         static double **partiallen = NULL;
      |                         ^~~~~~~~~~
getlag.c:165:25: warning: variable 'partialmtx' set but not used [-Wunused-but-set-variable]
  165 |         static double **partialmtx = NULL;
      |                         ^~~~~~~~~~
getlag.c:162:16: warning: variable 'pscore' set but not used [-Wunused-but-set-variable]
  162 |         double pscore;
      |                ^~~~~~
getlag.c: In function 'WriteOptions':
getlag.c:282:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
  282 |     else
      |     ^~~~
getlag.c:285:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
  285 |         if( alg == 'a' )
      |         ^~
getlag.c: In function 'main':
getlag.c:335:34: warning: variable 'node1' set but not used [-Wunused-but-set-variable]
  335 |         static double **node0, **node1;
      |                                  ^~~~~
gcc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o Dalignmm.o getlag.o defs.o fft.o fftFunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:959:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  959 |         *gaptable1 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2057:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
In function 'Atracking',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2067:9:
Salignmm.c:961:20: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  961 |         *gaptable2 = 0;
      |                    ^
In function 'AllocateCharVec',
    inlined from 'A__align.constprop.isra' at Salignmm.c:2058:16:
mtxutl.c:37:24: note: at offset [-4294967296, -2] into destination object of size [0, 2147483647] allocated by 'calloc'
   37 |         cvec = (char *)calloc( l1, sizeof( char ) );
      |                        ^
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c dndpre.c
dndpre.c: In function 'main':
dndpre.c:517:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
  517 |         if( skiptable ) FreeIntMtx( skiptable ); skiptable = NULL;
      |         ^~
dndpre.c:517:50: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
  517 |         if( skiptable ) FreeIntMtx( skiptable ); skiptable = NULL;
      |                                                  ^~~~~~~~~
gcc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c setcore.c
setcore.c: In function 'main':
setcore.c:288:34: warning: variable 'node1' set but not used [-Wunused-but-set-variable]
  288 |         static double **node0, **node1;
      |                                  ^~~~~
gcc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o fftFunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -c -o filter.o filter.c
filter.c: In function 'count_unusual':
filter.c:11:20: warning: unused variable 'len' [-Wunused-variable]
   11 |         int count, len;
      |                    ^~~
filter.c:9:13: warning: unused variable 'i' [-Wunused-variable]
    9 |         int i;
      |             ^
filter.c: In function 'shortenN':
filter.c:26:13: warning: unused variable 'i' [-Wunused-variable]
   26 |         int i;
      |             ^
gcc -o filter mtxutl.o io.o filter.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c replaceu.c
gcc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c restoreu.c
restoreu.c: In function 'main':
restoreu.c:185:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  185 |                         fgets( gett, 999, dlfp );
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~
restoreu.c:186:29: warning: 'dlfp' may be used uninitialized [-Wmaybe-uninitialized]
  186 |                         if( feof( dlfp ) ) break;
      |                             ^~~~~~~~~~~~
restoreu.c:91:15: note: 'dlfp' was declared here
   91 |         FILE *dlfp;
      |               ^~~~
gcc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c setdirection.c
setdirection.c: In function 'main':
setdirection.c:132:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result]
  132 |                 fgets( line, 99, difp );
      |                 ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:964,
                 from mltaln.h:12,
                 from setdirection.c:1:
In function 'fgets',
    inlined from 'main' at setdirection.c:132:3:
/usr/include/bits/stdio2.h:213:12: warning: 'difp' may be used uninitialized [-Wmaybe-uninitialized]
  213 |     return __fgets_alias (__s, __n, __stream);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
setdirection.c: In function 'main':
setdirection.c:66:15: note: 'difp' was declared here
   66 |         FILE *difp;
      |               ^~~~
gcc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -c makedirectionlist.c
makedirectionlist.c: In function 'directionthread':
makedirectionlist.c:646:34: warning: 'mseq1' may be used uninitialized [-Wmaybe-uninitialized]
  646 |                         res[j] = L__align11_noalign( n_dis_consweight_multi, mseq1, mseq2 );
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
makedirectionlist.c:600:16: note: 'mseq1' was declared here
  600 |         char **mseq1, **mseq2;
      |                ^~~~~
makedirectionlist.c:646:34: warning: 'mseq2' may be used uninitialized [-Wmaybe-uninitialized]
  646 |                         res[j] = L__align11_noalign( n_dis_consweight_multi, mseq1, mseq2 );
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
makedirectionlist.c:600:25: note: 'mseq2' was declared here
  600 |         char **mseq1, **mseq2;
      |                         ^~~~~
makedirectionlist.c: In function 'main':
makedirectionlist.c:891:33: warning: 'pointt' may be used uninitialized [-Wmaybe-uninitialized]
  891 |                                 makepointtable_nuc( pointt[i], grpseq );
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
makedirectionlist.c:683:16: note: 'pointt' was declared here
  683 |         int  **pointt, **pointt_rev, **spointt;
      |                ^~~~~~
makedirectionlist.c:909:33: warning: 'pointt_rev' may be used uninitialized [-Wmaybe-uninitialized]
  909 |                                 makepointtable_nuc( pointt_rev[i], grpseq );
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
makedirectionlist.c:683:26: note: 'pointt_rev' was declared here
  683 |         int  **pointt, **pointt_rev, **spointt;
      |                          ^~~~~~~~~~
makedirectionlist.c:892:44: warning: 'spointt' may be used uninitialized [-Wmaybe-uninitialized]
  892 |                                 spointt[i] = pointt[i];
      |                                 ~~~~~~~~~~~^~~~~~~~~~~
makedirectionlist.c:683:40: note: 'spointt' was declared here
  683 |         int  **pointt, **pointt_rev, **spointt;
      |                                        ^~~~~~~
gcc -o makedirectionlist mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o  Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread
gcc -o version version.c  -Denablemultithread  -std=c99 -fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -lm  -lpthread 
sed "s:_LIBDIR:/usr/local/libexec/mafft:" mafft.tmpl  > mafft
sed "s:_BINDIR:/usr/local/bin:" mafft-homologs.tmpl  > mafft-homologs.rb
sed "s:_BINDIR:/usr/local/bin:" mafft-sparsecore.tmpl  > mafft-sparsecore.rb
cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts
chmod 755 ../scripts/*
cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  ../binaries
chmod 755 ../binaries/*
done.
+ cd ../extensions
+ make clean
rm -f *.o *.a *.exe *~ mxscarnamod
make clean -C mxscarna_src
make[1]: Entering directory '/builddir/build/BUILD/mafft-v7.520/extensions/mxscarna_src'
rm -f mxscarna  *.o *.h~ *.hpp~ *.cpp~ *.cc~ ./vienna/*.o 
make -C ./probconsRNA clean
make[2]: Entering directory '/builddir/build/BUILD/mafft-v7.520/extensions/mxscarna_src/probconsRNA'
rm -f probcons 
make[2]: Leaving directory '/builddir/build/BUILD/mafft-v7.520/extensions/mxscarna_src/probconsRNA'
make[1]: Leaving directory '/builddir/build/BUILD/mafft-v7.520/extensions/mxscarna_src'
+ make 'CFLAGS=-fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
make CFLAGS1="" -C mxscarna_src
make[1]: Entering directory '/builddir/build/BUILD/mafft-v7.520/extensions/mxscarna_src'
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c Main.cc -o Main.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c McCaskill.cpp -o McCaskill.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c ./vienna/energy_param.cpp -o ./vienna/energy_param.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c seq2scs.cpp -o seq2scs.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c Globaldp.cpp -o Globaldp.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c postProcessings.cpp -o postProcessings.o
g++ -I./probconsRNA -I./vienna -I./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -c AlifoldMEA.cpp -o AlifoldMEA.o
g++ -L./probconsRNA  -L./ -DNDEBUG -DNumInsertStates=1 -DVERSION="2.0" -O3    -std=c++98 -lm -o mxscarna Main.o McCaskill.o vienna/energy_param.o seq2scs.o Globaldp.o postProcessings.o AlifoldMEA.o
make[1]: Leaving directory '/builddir/build/BUILD/mafft-v7.520/extensions/mxscarna_src'
mv mxscarna_src/mxscarna mxscarnamod
cp mxscarnamod ../binaries
chmod 755 ../binaries/*
done.
+ cd ..
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.HbfFdL
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64
++ dirname /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd mafft-v7.520
+ rm -rf '%{buidroot}'
+ cd core
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64 'INSTALL=/usr/bin/install -p' 'CFLAGS=-fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts
chmod 755 ../scripts/*
cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  ../binaries
chmod 755 ../binaries/*
done.
mkdir -p /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/libexec/mafft
chmod 755 /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/libexec/mafft
mkdir -p /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/bin
chmod 755 /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/bin
chmod 755 mafft mafft-homologs.rb mafft-sparsecore.rb
/usr/bin/install -p mafft mafft-homologs.rb mafft-sparsecore.rb  /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/bin
chmod 755 dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  ||:     # in MinGW, it's ok if this fails
strip dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  ||: # may fail for dash_client on mac.
/usr/bin/install -p dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version  /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/libexec/mafft
/usr/bin/install -p mafftash_premafft.pl seekquencer_premafft.pl /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/libexec/mafft
( cd /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/bin; \
rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi mafft-randomcore.rb ; \
ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \
ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \
ln -s mafft einsi; \
ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \
ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \
ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\
rm -f mafft-profile mafft-profile.exe; ln -s /usr/local/libexec/mafft/mafft-profile .; \
rm -f mafft-distance mafft-distance.exe; ln -s /usr/local/libexec/mafft/mafft-distance . )
mkdir -p /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/share/man/man1
chmod 755 /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/share/man/man1
/usr/bin/install -p -m 644 mafft.1 mafft-homologs.1 /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/share/man/man1
+ cd ../extensions
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64 'INSTALL=/usr/bin/install -p' 'CFLAGS=-fPIE -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64   -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
cp mxscarnamod ../binaries
chmod 755 ../binaries/*
done.
mkdir -p /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/libexec/mafft
chmod 755 /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/libexec/mafft
chmod 755 mxscarnamod
/usr/bin/install -p mxscarnamod /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64/usr/local/libexec/mafft
+ cd ..
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip /usr/bin/strip
+ /usr/lib/rpm/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump
+ /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/local/bin/mafft-sparsecore.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/local/bin/mafft-homologs.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/local/bin/mafft 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
Processing files: mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64
warning: absolute symlink: /usr/local/bin/mafft-distance -> /usr/local/libexec/mafft/mafft-distance
warning: absolute symlink: /usr/local/bin/mafft-profile -> /usr/local/libexec/mafft/mafft-profile
Provides: mafft = 7.520-1.20230516222539466786.mafft.fc39 mafft(x86-64) = 7.520-1.20230516222539466786.mafft.fc39
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 glibc >= 2.37.9000-9 libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.27)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) rtld(GNU_HASH)
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64
Wrote: /builddir/build/RPMS/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.DB6mvv
+ umask 022
+ cd /builddir/build/BUILD
+ cd mafft-v7.520
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/mafft-7.520-1.20230516222539466786.mafft.fc39.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.Q2b3NE
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf mafft-v7.520 mafft-v7.520.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0

RPM build warnings:
    absolute symlink: /usr/local/bin/mafft-distance -> /usr/local/libexec/mafft/mafft-distance
    absolute symlink: /usr/local/bin/mafft-profile -> /usr/local/libexec/mafft/mafft-profile
Finish: rpmbuild mafft-7.520-1.20230516222539466786.mafft.fc39.src.rpm
Finish: build phase for mafft-7.520-1.20230516222539466786.mafft.fc39.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1684275986.169171/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-x86_64-1684275986.169171/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-x86_64-1684275986.169171/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/mafft-7.520-1.20230516222539466786.mafft.fc39.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