Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c14a' (ED25519) to the list of known hosts.
Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5925871 --chroot fedora-38-x86_64 --detached
Version: 0.64
PID: 7259
Logging PID: 7260
Task:
{'appstream': False,
 'background': False,
 'build_id': 5925871,
 'buildroot_pkgs': [],
 'chroot': 'fedora-38-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '9858ffad1833b26b7a06a461001af2071dc88114',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/fi-muni/bioinformatics-pull-requests/mafft',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'mafft',
 'package_version': '7.520-1.20230516221152439026.pr1',
 'project_dirname': 'bioinformatics-pull-requests',
 'project_name': 'bioinformatics-pull-requests',
 'project_owner': 'fi-muni',
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/fi-muni/bioinformatics-pull-requests/fedora-38-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository'}],
 'sandbox': 'fi-muni/bioinformatics-pull-requests--packit',
 'source_json': {},
 'source_type': None,
 'submitter': 'packit',
 'tags': [],
 'task_id': '5925871-fedora-38-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-pull-requests/mafft /var/lib/copr-rpmbuild/workspace/workdir-4nnaj2wf/mafft --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/fi-muni/bioinformatics-pull-requests/mafft', '/var/lib/copr-rpmbuild/workspace/workdir-4nnaj2wf/mafft', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-4nnaj2wf/mafft'...

Running: git checkout 9858ffad1833b26b7a06a461001af2071dc88114

cmd: ['git', 'checkout', '9858ffad1833b26b7a06a461001af2071dc88114']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-4nnaj2wf/mafft
rc: 0
stdout: 
stderr: Note: switching to '9858ffad1833b26b7a06a461001af2071dc88114'.

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 9858ffa automatic import of mafft

Running: copr-distgit-client sources

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-4nnaj2wf/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-pull-requests/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  7289k      0 --:--:-- --:--:-- --:--:-- 7300k
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-4nnaj2wf/mafft/mafft.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-4nnaj2wf/mafft --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1684275155.629876 -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-4nnaj2wf/mafft/mafft.spec)  Config(fedora-38-x86_64)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-38-x86_64-bootstrap-1684275155.629876/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                                 734  B/s | 257  B     00:00    
fedora                                           27 MB/s |  83 MB     00:03    
updates                                          14 MB/s |  17 MB     00:01    
Dependencies resolved.
================================================================================
 Package                       Arch   Version                     Repo     Size
================================================================================
Installing:
 dnf                           noarch 4.15.0-1.fc38               updates 476 k
 dnf-plugins-core              noarch 4.4.0-1.fc38                fedora   38 k
Installing dependencies:
 alternatives                  x86_64 1.24-1.fc38                 updates  39 k
 audit-libs                    x86_64 3.1.1-1.fc38                updates 116 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 9.1-12.fc38                 updates 1.1 M
 coreutils-common              x86_64 9.1-12.fc38                 updates 2.0 M
 crypto-policies               noarch 20230301-1.gita12f7b2.fc38  fedora   93 k
 curl                          x86_64 8.0.1-1.fc38                updates 350 k
 cyrus-sasl-lib                x86_64 2.1.28-9.fc38               fedora  794 k
 dbus-libs                     x86_64 1:1.14.6-1.fc38             fedora  156 k
 dnf-data                      noarch 4.15.0-1.fc38               updates  39 k
 elfutils-default-yama-scope   noarch 0.189-2.fc38                updates  15 k
 elfutils-libelf               x86_64 0.189-2.fc38                updates 196 k
 elfutils-libs                 x86_64 0.189-2.fc38                updates 260 k
 expat                         x86_64 2.5.0-2.fc38                fedora  110 k
 fedora-gpg-keys               noarch 38-1                        fedora  126 k
 fedora-release                noarch 38-35                       updates  12 k
 fedora-release-common         noarch 38-35                       updates  22 k
 fedora-release-identity-basic noarch 38-35                       updates  13 k
 fedora-repos                  noarch 38-1                        fedora  9.1 k
 file-libs                     x86_64 5.44-3.fc38                 fedora  730 k
 filesystem                    x86_64 3.18-3.fc38                 fedora  1.1 M
 findutils                     x86_64 1:4.9.0-3.fc38              fedora  492 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.fc38               updates 2.8 M
 glibc                         x86_64 2.37-4.fc38                 updates 2.1 M
 glibc-common                  x86_64 2.37-4.fc38                 updates 314 k
 glibc-minimal-langpack        x86_64 2.37-4.fc38                 updates  37 k
 gmp                           x86_64 1:6.2.1-4.fc38              fedora  313 k
 gnupg2                        x86_64 2.4.0-3.fc38                fedora  2.6 M
 gnutls                        x86_64 3.8.0-2.fc38                fedora  1.1 M
 gpgme                         x86_64 1.17.1-3.fc38               fedora  210 k
 grep                          x86_64 3.8-3.fc38                  fedora  293 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 1.20.1-8.fc38               fedora  727 k
 libacl                        x86_64 2.3.1-6.fc38                fedora   23 k
 libarchive                    x86_64 3.6.1-4.fc38                fedora  400 k
 libassuan                     x86_64 2.5.5-6.fc38                fedora   67 k
 libattr                       x86_64 2.5.1-6.fc38                fedora   18 k
 libb2                         x86_64 0.98.1-8.fc38               fedora   25 k
 libblkid                      x86_64 2.38.1-4.fc38               fedora  106 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 0.1.18-6.fc38               fedora   77 k
 libcurl                       x86_64 8.0.1-1.fc38                updates 313 k
 libdnf                        x86_64 0.70.0-1.fc38               fedora  660 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.fc38               updates 106 k
 libgcrypt                     x86_64 1.10.2-1.fc38               updates 514 k
 libgomp                       x86_64 13.1.1-2.fc38               updates 316 k
 libgpg-error                  x86_64 1.47-1.fc38                 updates 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.fc38               updates 231 k
 libmount                      x86_64 2.38.1-4.fc38               fedora  135 k
 libnghttp2                    x86_64 1.52.0-1.fc38               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.fc38              updates  14 k
 libselinux                    x86_64 3.5-1.fc38                  fedora   87 k
 libsemanage                   x86_64 3.5-2.fc38                  fedora  120 k
 libsepol                      x86_64 3.5-1.fc38                  fedora  324 k
 libsigsegv                    x86_64 2.14-4.fc38                 fedora   27 k
 libsmartcols                  x86_64 2.38.1-4.fc38               fedora   64 k
 libsolv                       x86_64 0.7.22-4.fc38               fedora  412 k
 libssh                        x86_64 0.10.5-1.fc38               updates 211 k
 libssh-config                 noarch 0.10.5-1.fc38               updates 9.0 k
 libstdc++                     x86_64 13.1.1-2.fc38               updates 860 k
 libtasn1                      x86_64 4.19.0-2.fc38               fedora   74 k
 libtirpc                      x86_64 1.3.3-1.rc1.fc38            updates  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 2.38.1-4.fc38               fedora   28 k
 libverto                      x86_64 0.3.2-5.fc38                fedora   21 k
 libxcrypt                     x86_64 4.4.33-7.fc38               fedora  120 k
 libxml2                       x86_64 2.10.4-1.fc38               updates 701 k
 libyaml                       x86_64 0.2.5-9.fc38                fedora   59 k
 libzstd                       x86_64 1.5.5-1.fc38                updates 308 k
 lua-libs                      x86_64 5.4.4-9.fc38                fedora  133 k
 lz4-libs                      x86_64 1.9.4-2.fc38                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 2.6.4-1.fc38                fedora  254 k
 openssl-libs                  x86_64 1:3.0.8-2.fc38              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.fc38             fedora   60 k
 python-pip-wheel              noarch 22.3.1-2.fc38               fedora  1.4 M
 python-setuptools-wheel       noarch 65.5.1-2.fc38               fedora  715 k
 python3                       x86_64 3.11.3-1.fc38               updates  28 k
 python3-dateutil              noarch 1:2.8.2-5.fc38              fedora  360 k
 python3-dbus                  x86_64 1.3.2-2.fc38                fedora  157 k
 python3-distro                noarch 1.8.0-2.fc38                fedora   49 k
 python3-dnf                   noarch 4.15.0-1.fc38               updates 603 k
 python3-dnf-plugins-core      noarch 4.4.0-1.fc38                fedora  298 k
 python3-gpg                   x86_64 1.17.1-3.fc38               fedora  296 k
 python3-hawkey                x86_64 0.70.0-1.fc38               fedora  106 k
 python3-libcomps              x86_64 0.1.18-6.fc38               fedora   47 k
 python3-libdnf                x86_64 0.70.0-1.fc38               fedora  822 k
 python3-libs                  x86_64 3.11.3-1.fc38               updates 9.6 M
 python3-rpm                   x86_64 4.18.1-3.fc38               updates  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.fc38               updates 570 k
 rpm-build-libs                x86_64 4.18.1-3.fc38               updates  94 k
 rpm-libs                      x86_64 4.18.1-3.fc38               updates 313 k
 rpm-sequoia                   x86_64 1.4.0-2.fc38                updates 850 k
 rpm-sign-libs                 x86_64 4.18.1-3.fc38               updates  26 k
 sed                           x86_64 4.8-12.fc38                 fedora  306 k
 setup                         noarch 2.14.3-2.fc38               fedora  152 k
 shadow-utils                  x86_64 2:4.13-6.fc38               fedora  1.3 M
 sqlite-libs                   x86_64 3.40.1-2.fc38               fedora  666 k
 systemd-libs                  x86_64 253.4-1.fc38                updates 652 k
 tpm2-tss                      x86_64 4.0.1-3.fc38                fedora  675 k
 tzdata                        noarch 2023c-1.fc38                fedora  718 k
 xz-libs                       x86_64 5.4.1-1.fc38                fedora  108 k
 zchunk-libs                   x86_64 1.3.1-1.fc38                updates  52 k
 zlib                          x86_64 1.2.13-3.fc38               fedora   95 k

Transaction Summary
================================================================================
Install  139 Packages

Total download size: 58 M
Installed size: 203 M
Downloading Packages:
(1/139): basesystem-11-15.fc38.noarch.rpm        25 kB/s | 7.0 kB     00:00    
(2/139): bzip2-libs-1.0.8-13.fc38.x86_64.rpm     93 kB/s |  41 kB     00:00    
(3/139): ca-certificates-2023.2.60-2.fc38.noarc 977 kB/s | 845 kB     00:00    
(4/139): cyrus-sasl-lib-2.1.28-9.fc38.x86_64.rp 910 kB/s | 794 kB     00:00    
(5/139): dbus-libs-1.14.6-1.fc38.x86_64.rpm     513 kB/s | 156 kB     00:00    
(6/139): dnf-plugins-core-4.4.0-1.fc38.noarch.r 249 kB/s |  38 kB     00:00    
(7/139): crypto-policies-20230301-1.gita12f7b2.  43 kB/s |  93 kB     00:02    
(8/139): expat-2.5.0-2.fc38.x86_64.rpm          487 kB/s | 110 kB     00:00    
(9/139): fedora-repos-38-1.noarch.rpm            24 kB/s | 9.1 kB     00:00    
(10/139): fedora-gpg-keys-38-1.noarch.rpm       210 kB/s | 126 kB     00:00    
(11/139): file-libs-5.44-3.fc38.x86_64.rpm      820 kB/s | 730 kB     00:00    
(12/139): bash-5.2.15-3.fc38.x86_64.rpm         456 kB/s | 1.8 MB     00:04    
(13/139): findutils-4.9.0-3.fc38.x86_64.rpm     668 kB/s | 492 kB     00:00    
(14/139): gawk-5.1.1-5.fc38.x86_64.rpm          1.0 MB/s | 1.0 MB     00:00    
(15/139): filesystem-3.18-3.fc38.x86_64.rpm     566 kB/s | 1.1 MB     00:01    
(16/139): gmp-6.2.1-4.fc38.x86_64.rpm           1.1 MB/s | 313 kB     00:00    
(17/139): gdbm-libs-1.23-3.fc38.x86_64.rpm       50 kB/s |  56 kB     00:01    
(18/139): gpgme-1.17.1-3.fc38.x86_64.rpm        452 kB/s | 210 kB     00:00    
(19/139): gnutls-3.8.0-2.fc38.x86_64.rpm        1.0 MB/s | 1.1 MB     00:01    
(20/139): ima-evm-utils-1.4-7.fc38.x86_64.rpm   134 kB/s |  62 kB     00:00    
(21/139): json-c-0.16-4.fc38.x86_64.rpm         171 kB/s |  41 kB     00:00    
(22/139): grep-3.8-3.fc38.x86_64.rpm            311 kB/s | 293 kB     00:00    
(23/139): keyutils-libs-1.6.1-6.fc38.x86_64.rpm 176 kB/s |  31 kB     00:00    
(24/139): libacl-2.3.1-6.fc38.x86_64.rpm        198 kB/s |  23 kB     00:00    
(25/139): libarchive-3.6.1-4.fc38.x86_64.rpm    885 kB/s | 400 kB     00:00    
(26/139): libassuan-2.5.5-6.fc38.x86_64.rpm     362 kB/s |  67 kB     00:00    
(27/139): libattr-2.5.1-6.fc38.x86_64.rpm       104 kB/s |  18 kB     00:00    
(28/139): libb2-0.98.1-8.fc38.x86_64.rpm        212 kB/s |  25 kB     00:00    
(29/139): krb5-libs-1.20.1-8.fc38.x86_64.rpm    450 kB/s | 727 kB     00:01    
(30/139): libblkid-2.38.1-4.fc38.x86_64.rpm      92 kB/s | 106 kB     00:01    
(31/139): libcap-2.48-6.fc38.x86_64.rpm         362 kB/s |  67 kB     00:00    
(32/139): libbrotli-1.0.9-11.fc38.x86_64.rpm    361 kB/s | 317 kB     00:00    
(33/139): libcap-ng-0.8.3-5.fc38.x86_64.rpm     138 kB/s |  32 kB     00:00    
(34/139): libcom_err-1.46.5-4.fc38.x86_64.rpm   128 kB/s |  26 kB     00:00    
(35/139): libcomps-0.1.18-6.fc38.x86_64.rpm     389 kB/s |  77 kB     00:00    
(36/139): libeconf-0.4.0-5.fc38.x86_64.rpm      216 kB/s |  27 kB     00:00    
(37/139): gnupg2-2.4.0-3.fc38.x86_64.rpm        468 kB/s | 2.6 MB     00:05    
(38/139): libevent-2.1.12-8.fc38.x86_64.rpm     347 kB/s | 257 kB     00:00    
(39/139): libffi-3.4.4-2.fc38.x86_64.rpm        196 kB/s |  38 kB     00:00    
(40/139): libidn2-2.3.4-2.fc38.x86_64.rpm       295 kB/s | 160 kB     00:00    
(41/139): libfsverity-1.4-9.fc38.x86_64.rpm      19 kB/s |  19 kB     00:01    
(42/139): libdnf-0.70.0-1.fc38.x86_64.rpm       313 kB/s | 660 kB     00:02    
(43/139): libksba-1.6.3-2.fc38.x86_64.rpm       245 kB/s | 159 kB     00:00    
(44/139): libmount-2.38.1-4.fc38.x86_64.rpm     484 kB/s | 135 kB     00:00    
(45/139): libnsl2-2.0.0-5.fc38.x86_64.rpm       186 kB/s |  30 kB     00:00    
(46/139): libpsl-0.21.2-2.fc38.x86_64.rpm       270 kB/s |  65 kB     00:00    
(47/139): librepo-1.15.1-2.fc38.x86_64.rpm      218 kB/s |  96 kB     00:00    
(48/139): libnghttp2-1.52.0-1.fc38.x86_64.rpm    87 kB/s |  75 kB     00:00    
(49/139): libselinux-3.5-1.fc38.x86_64.rpm      153 kB/s |  87 kB     00:00    
(50/139): libsemanage-3.5-2.fc38.x86_64.rpm     267 kB/s | 120 kB     00:00    
(51/139): libsigsegv-2.14-4.fc38.x86_64.rpm     114 kB/s |  27 kB     00:00    
(52/139): libsmartcols-2.38.1-4.fc38.x86_64.rpm 206 kB/s |  64 kB     00:00    
(53/139): libtasn1-4.19.0-2.fc38.x86_64.rpm     249 kB/s |  74 kB     00:00    
(54/139): libsolv-0.7.22-4.fc38.x86_64.rpm      263 kB/s | 412 kB     00:01    
(55/139): libsepol-3.5-1.fc38.x86_64.rpm        120 kB/s | 324 kB     00:02    
(56/139): libuuid-2.38.1-4.fc38.x86_64.rpm       89 kB/s |  28 kB     00:00    
(57/139): libverto-0.3.2-5.fc38.x86_64.rpm      152 kB/s |  21 kB     00:00    
(58/139): libxcrypt-4.4.33-7.fc38.x86_64.rpm    346 kB/s | 120 kB     00:00    
(59/139): libyaml-0.2.5-9.fc38.x86_64.rpm       242 kB/s |  59 kB     00:00    
(60/139): libunistring1.0-1.0-1.fc38.x86_64.rpm 274 kB/s | 539 kB     00:01    
(61/139): lua-libs-5.4.4-9.fc38.x86_64.rpm      327 kB/s | 133 kB     00:00    
(62/139): libunistring-1.1-3.fc38.x86_64.rpm    167 kB/s | 545 kB     00:03    
(63/139): lz4-libs-1.9.4-2.fc38.x86_64.rpm      202 kB/s |  67 kB     00:00    
(64/139): mpdecimal-2.5.1-6.fc38.x86_64.rpm     307 kB/s |  89 kB     00:00    
(65/139): ncurses-base-6.4-3.20230114.fc38.noar 130 kB/s |  87 kB     00:00    
(66/139): ncurses-libs-6.4-3.20230114.fc38.x86_ 281 kB/s | 333 kB     00:01    
(67/139): npth-1.6-12.fc38.x86_64.rpm           114 kB/s |  24 kB     00:00    
(68/139): mpfr-4.1.1-3.fc38.x86_64.rpm          312 kB/s | 600 kB     00:01    
(69/139): nettle-3.8-3.fc38.x86_64.rpm          253 kB/s | 412 kB     00:01    
(70/139): openldap-2.6.4-1.fc38.x86_64.rpm      295 kB/s | 254 kB     00:00    
(71/139): p11-kit-trust-0.24.1-6.fc38.x86_64.rp 163 kB/s | 136 kB     00:00    
(72/139): p11-kit-0.24.1-6.fc38.x86_64.rpm      221 kB/s | 359 kB     00:01    
(73/139): pcre2-10.42-1.fc38.1.x86_64.rpm       282 kB/s | 234 kB     00:00    
(74/139): popt-1.19-2.fc38.x86_64.rpm           250 kB/s |  67 kB     00:00    
(75/139): publicsuffix-list-dafsa-20230318-1.fc 182 kB/s |  60 kB     00:00    
(76/139): pcre2-syntax-10.42-1.fc38.1.noarch.rp 148 kB/s | 144 kB     00:00    
(77/139): python-setuptools-wheel-65.5.1-2.fc38 134 kB/s | 715 kB     00:05    
(78/139): python3-dateutil-2.8.2-5.fc38.noarch. 199 kB/s | 360 kB     00:01    
(79/139): python3-dbus-1.3.2-2.fc38.x86_64.rpm  549 kB/s | 157 kB     00:00    
(80/139): python-pip-wheel-22.3.1-2.fc38.noarch 190 kB/s | 1.4 MB     00:07    
(81/139): python3-distro-1.8.0-2.fc38.noarch.rp 196 kB/s |  49 kB     00:00    
(82/139): openssl-libs-3.0.8-2.fc38.x86_64.rpm  192 kB/s | 2.1 MB     00:11    
(83/139): python3-gpg-1.17.1-3.fc38.x86_64.rpm  376 kB/s | 296 kB     00:00    
(84/139): python3-libcomps-0.1.18-6.fc38.x86_64 255 kB/s |  47 kB     00:00    
(85/139): python3-dnf-plugins-core-4.4.0-1.fc38 142 kB/s | 298 kB     00:02    
(86/139): python3-six-1.16.0-9.fc38.noarch.rpm  111 kB/s |  42 kB     00:00    
(87/139): python3-hawkey-0.70.0-1.fc38.x86_64.r  59 kB/s | 106 kB     00:01    
(88/139): python3-libdnf-0.70.0-1.fc38.x86_64.r 538 kB/s | 822 kB     00:01    
(89/139): python3-systemd-235-2.fc38.x86_64.rpm 137 kB/s | 108 kB     00:00    
(90/139): readline-8.2-3.fc38.x86_64.rpm        292 kB/s | 212 kB     00:00    
(91/139): sed-4.8-12.fc38.x86_64.rpm            358 kB/s | 306 kB     00:00    
(92/139): setup-2.14.3-2.fc38.noarch.rpm        139 kB/s | 152 kB     00:01    
(93/139): sqlite-libs-3.40.1-2.fc38.x86_64.rpm  562 kB/s | 666 kB     00:01    
(94/139): tzdata-2023c-1.fc38.noarch.rpm        411 kB/s | 718 kB     00:01    
(95/139): xz-libs-5.4.1-1.fc38.x86_64.rpm       130 kB/s | 108 kB     00:00    
(96/139): zlib-1.2.13-3.fc38.x86_64.rpm         150 kB/s |  95 kB     00:00    
(97/139): alternatives-1.24-1.fc38.x86_64.rpm   174 kB/s |  39 kB     00:00    
(98/139): audit-libs-3.1.1-1.fc38.x86_64.rpm    864 kB/s | 116 kB     00:00    
(99/139): coreutils-9.1-12.fc38.x86_64.rpm      4.6 MB/s | 1.1 MB     00:00    
(100/139): coreutils-common-9.1-12.fc38.x86_64.  15 MB/s | 2.0 MB     00:00    
(101/139): curl-8.0.1-1.fc38.x86_64.rpm         7.2 MB/s | 350 kB     00:00    
(102/139): dnf-4.15.0-1.fc38.noarch.rpm         9.5 MB/s | 476 kB     00:00    
(103/139): dnf-data-4.15.0-1.fc38.noarch.rpm    893 kB/s |  39 kB     00:00    
(104/139): elfutils-default-yama-scope-0.189-2. 342 kB/s |  15 kB     00:00    
(105/139): elfutils-libelf-0.189-2.fc38.x86_64. 4.2 MB/s | 196 kB     00:00    
(106/139): elfutils-libs-0.189-2.fc38.x86_64.rp 5.5 MB/s | 260 kB     00:00    
(107/139): fedora-release-38-35.noarch.rpm      286 kB/s |  12 kB     00:00    
(108/139): fedora-release-common-38-35.noarch.r 517 kB/s |  22 kB     00:00    
(109/139): fedora-release-identity-basic-38-35. 304 kB/s |  13 kB     00:00    
(110/139): tpm2-tss-4.0.1-3.fc38.x86_64.rpm     141 kB/s | 675 kB     00:04    
(111/139): glib2-2.76.2-1.fc38.x86_64.rpm        34 MB/s | 2.8 MB     00:00    
(112/139): glibc-common-2.37-4.fc38.x86_64.rpm  6.7 MB/s | 314 kB     00:00    
(113/139): glibc-minimal-langpack-2.37-4.fc38.x 849 kB/s |  37 kB     00:00    
(114/139): libcurl-8.0.1-1.fc38.x86_64.rpm      6.7 MB/s | 313 kB     00:00    
(115/139): shadow-utils-4.13-6.fc38.x86_64.rpm  216 kB/s | 1.3 MB     00:05    
(116/139): libgcc-13.1.1-2.fc38.x86_64.rpm      2.4 MB/s | 106 kB     00:00    
(117/139): libgomp-13.1.1-2.fc38.x86_64.rpm     6.6 MB/s | 316 kB     00:00    
(118/139): libgpg-error-1.47-1.fc38.x86_64.rpm  4.9 MB/s | 230 kB     00:00    
(119/139): libmodulemd-2.15.0-2.fc38.x86_64.rpm 4.6 MB/s | 231 kB     00:00    
(120/139): libreport-filesystem-2.17.10-1.fc38. 324 kB/s |  14 kB     00:00    
(121/139): libssh-0.10.5-1.fc38.x86_64.rpm      4.5 MB/s | 211 kB     00:00    
(122/139): glibc-2.37-4.fc38.x86_64.rpm         4.5 MB/s | 2.1 MB     00:00    
(123/139): libssh-config-0.10.5-1.fc38.noarch.r 210 kB/s | 9.0 kB     00:00    
(124/139): libstdc++-13.1.1-2.fc38.x86_64.rpm    15 MB/s | 860 kB     00:00    
(125/139): libtirpc-1.3.3-1.rc1.fc38.x86_64.rpm 2.1 MB/s |  93 kB     00:00    
(126/139): libgcrypt-1.10.2-1.fc38.x86_64.rpm   1.4 MB/s | 514 kB     00:00    
(127/139): libxml2-2.10.4-1.fc38.x86_64.rpm      13 MB/s | 701 kB     00:00    
(128/139): libzstd-1.5.5-1.fc38.x86_64.rpm      6.5 MB/s | 308 kB     00:00    
(129/139): python3-3.11.3-1.fc38.x86_64.rpm     635 kB/s |  28 kB     00:00    
(130/139): python3-dnf-4.15.0-1.fc38.noarch.rpm  11 MB/s | 603 kB     00:00    
(131/139): python3-rpm-4.18.1-3.fc38.x86_64.rpm 1.3 MB/s |  72 kB     00:00    
(132/139): rpm-4.18.1-3.fc38.x86_64.rpm          10 MB/s | 570 kB     00:00    
(133/139): rpm-build-libs-4.18.1-3.fc38.x86_64. 1.8 MB/s |  94 kB     00:00    
(134/139): rpm-libs-4.18.1-3.fc38.x86_64.rpm    6.1 MB/s | 313 kB     00:00    
(135/139): rpm-sign-libs-4.18.1-3.fc38.x86_64.r 590 kB/s |  26 kB     00:00    
(136/139): python3-libs-3.11.3-1.fc38.x86_64.rp  49 MB/s | 9.6 MB     00:00    
(137/139): rpm-sequoia-1.4.0-2.fc38.x86_64.rpm  8.8 MB/s | 850 kB     00:00    
(138/139): systemd-libs-253.4-1.fc38.x86_64.rpm  12 MB/s | 652 kB     00:00    
(139/139): zchunk-libs-1.3.1-1.fc38.x86_64.rpm  1.1 MB/s |  52 kB     00:00    
--------------------------------------------------------------------------------
Total                                           1.5 MB/s |  58 MB     00:39     
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-3.18-3.fc38.x86_64                          1/1 
  Preparing        :                                                        1/1 
  Installing       : libgcc-13.1.1-2.fc38.x86_64                          1/139 
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  Installing       : crypto-policies-20230301-1.gita12f7b2.fc38.noarc     3/139 
  Running scriptlet: crypto-policies-20230301-1.gita12f7b2.fc38.noarc     3/139 
  Installing       : fedora-release-identity-basic-38-35.noarch           4/139 
  Installing       : libssh-config-0.10.5-1.fc38.noarch                   5/139 
  Installing       : libreport-filesystem-2.17.10-1.fc38.noarch           6/139 
  Installing       : dnf-data-4.15.0-1.fc38.noarch                        7/139 
warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew

  Installing       : coreutils-common-9.1-12.fc38.x86_64                  8/139 
  Installing       : python-setuptools-wheel-65.5.1-2.fc38.noarch         9/139 
  Installing       : publicsuffix-list-dafsa-20230318-1.fc38.noarch      10/139 
  Installing       : pcre2-syntax-10.42-1.fc38.1.noarch                  11/139 
  Installing       : ncurses-base-6.4-3.20230114.fc38.noarch             12/139 
  Installing       : fedora-gpg-keys-38-1.noarch                         13/139 
  Installing       : fedora-release-38-35.noarch                         14/139 
  Installing       : fedora-repos-38-1.noarch                            15/139 
  Installing       : fedora-release-common-38-35.noarch                  16/139 
  Installing       : setup-2.14.3-2.fc38.noarch                          17/139 
  Running scriptlet: setup-2.14.3-2.fc38.noarch                          17/139 
  Installing       : filesystem-3.18-3.fc38.x86_64                       18/139 
  Installing       : basesystem-11-15.fc38.noarch                        19/139 
  Installing       : bash-5.2.15-3.fc38.x86_64                           20/139 
  Running scriptlet: bash-5.2.15-3.fc38.x86_64                           20/139 
  Installing       : ncurses-libs-6.4-3.20230114.fc38.x86_64             21/139 
  Installing       : glibc-common-2.37-4.fc38.x86_64                     22/139 
  Installing       : glibc-minimal-langpack-2.37-4.fc38.x86_64           23/139 
  Running scriptlet: glibc-2.37-4.fc38.x86_64                            24/139 
  Installing       : glibc-2.37-4.fc38.x86_64                            24/139 
  Running scriptlet: glibc-2.37-4.fc38.x86_64                            24/139 
  Installing       : zlib-1.2.13-3.fc38.x86_64                           25/139 
  Installing       : bzip2-libs-1.0.8-13.fc38.x86_64                     26/139 
  Installing       : xz-libs-5.4.1-1.fc38.x86_64                         27/139 
  Installing       : libzstd-1.5.5-1.fc38.x86_64                         28/139 
  Installing       : sqlite-libs-3.40.1-2.fc38.x86_64                    29/139 
  Installing       : libcap-2.48-6.fc38.x86_64                           30/139 
  Installing       : gmp-1:6.2.1-4.fc38.x86_64                           31/139 
  Installing       : popt-1.19-2.fc38.x86_64                             32/139 
  Installing       : libgpg-error-1.47-1.fc38.x86_64                     33/139 
  Installing       : libxml2-2.10.4-1.fc38.x86_64                        34/139 
  Installing       : libuuid-2.38.1-4.fc38.x86_64                        35/139 
  Installing       : lua-libs-5.4.4-9.fc38.x86_64                        36/139 
  Installing       : elfutils-libelf-0.189-2.fc38.x86_64                 37/139 
  Installing       : libattr-2.5.1-6.fc38.x86_64                         38/139 
  Installing       : libacl-2.3.1-6.fc38.x86_64                          39/139 
  Installing       : libffi-3.4.4-2.fc38.x86_64                          40/139 
  Installing       : p11-kit-0.24.1-6.fc38.x86_64                        41/139 
  Installing       : libxcrypt-4.4.33-7.fc38.x86_64                      42/139 
  Installing       : pcre2-10.42-1.fc38.1.x86_64                         43/139 
  Installing       : readline-8.2-3.fc38.x86_64                          44/139 
  Installing       : libstdc++-13.1.1-2.fc38.x86_64                      45/139 
  Installing       : libassuan-2.5.5-6.fc38.x86_64                       46/139 
  Installing       : file-libs-5.44-3.fc38.x86_64                        47/139 
  Installing       : expat-2.5.0-2.fc38.x86_64                           48/139 
  Installing       : gdbm-libs-1:1.23-3.fc38.x86_64                      49/139 
  Installing       : json-c-0.16-4.fc38.x86_64                           50/139 
  Installing       : keyutils-libs-1.6.1-6.fc38.x86_64                   51/139 
  Installing       : libcom_err-1.46.5-4.fc38.x86_64                     52/139 
  Installing       : libsepol-3.5-1.fc38.x86_64                          53/139 
  Installing       : libselinux-3.5-1.fc38.x86_64                        54/139 
  Installing       : sed-4.8-12.fc38.x86_64                              55/139 
  Installing       : libsmartcols-2.38.1-4.fc38.x86_64                   56/139 
  Installing       : libtasn1-4.19.0-2.fc38.x86_64                       57/139 
  Installing       : libunistring1.0-1.0-1.fc38.x86_64                   58/139 
  Installing       : libidn2-2.3.4-2.fc38.x86_64                         59/139 
  Installing       : lz4-libs-1.9.4-2.fc38.x86_64                        60/139 
  Installing       : systemd-libs-253.4-1.fc38.x86_64                    61/139 
  Installing       : libgomp-13.1.1-2.fc38.x86_64                        62/139 
  Installing       : libb2-0.98.1-8.fc38.x86_64                          63/139 
  Installing       : dbus-libs-1:1.14.6-1.fc38.x86_64                    64/139 
  Installing       : libpsl-0.21.2-2.fc38.x86_64                         65/139 
  Installing       : findutils-1:4.9.0-3.fc38.x86_64                     66/139 
  Installing       : cyrus-sasl-lib-2.1.28-9.fc38.x86_64                 67/139 
  Installing       : libcomps-0.1.18-6.fc38.x86_64                       68/139 
  Installing       : grep-3.8-3.fc38.x86_64                              69/139 
  Installing       : libblkid-2.38.1-4.fc38.x86_64                       70/139 
  Installing       : libmount-2.38.1-4.fc38.x86_64                       71/139 
  Installing       : libksba-1.6.3-2.fc38.x86_64                         72/139 
  Installing       : libgcrypt-1.10.2-1.fc38.x86_64                      73/139 
  Installing       : mpfr-4.1.1-3.fc38.x86_64                            74/139 
  Installing       : nettle-3.8-3.fc38.x86_64                            75/139 
  Installing       : libbrotli-1.0.9-11.fc38.x86_64                      76/139 
  Installing       : libcap-ng-0.8.3-5.fc38.x86_64                       77/139 
  Installing       : audit-libs-3.1.1-1.fc38.x86_64                      78/139 
  Installing       : libsemanage-3.5-2.fc38.x86_64                       79/139 
  Installing       : libeconf-0.4.0-5.fc38.x86_64                        80/139 
  Installing       : shadow-utils-2:4.13-6.fc38.x86_64                   81/139 
  Installing       : libnghttp2-1.52.0-1.fc38.x86_64                     82/139 
  Installing       : libsigsegv-2.14-4.fc38.x86_64                       83/139 
  Installing       : gawk-5.1.1-5.fc38.x86_64                            84/139 
  Installing       : libunistring-1.1-3.fc38.x86_64                      85/139 
  Installing       : libverto-0.3.2-5.fc38.x86_64                        86/139 
  Installing       : libyaml-0.2.5-9.fc38.x86_64                         87/139 
  Installing       : mpdecimal-2.5.1-6.fc38.x86_64                       88/139 
  Installing       : npth-1.6-12.fc38.x86_64                             89/139 
  Installing       : alternatives-1.24-1.fc38.x86_64                     90/139 
  Installing       : p11-kit-trust-0.24.1-6.fc38.x86_64                  91/139 
  Running scriptlet: p11-kit-trust-0.24.1-6.fc38.x86_64                  91/139 
  Installing       : openssl-libs-1:3.0.8-2.fc38.x86_64                  92/139 
  Installing       : coreutils-9.1-12.fc38.x86_64                        93/139 
  Running scriptlet: ca-certificates-2023.2.60-2.fc38.noarch             94/139 
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  Installing       : rpm-sequoia-1.4.0-2.fc38.x86_64                     95/139 
  Installing       : rpm-libs-4.18.1-3.fc38.x86_64                       96/139 
  Installing       : krb5-libs-1.20.1-8.fc38.x86_64                      97/139 
  Installing       : libtirpc-1.3.3-1.rc1.fc38.x86_64                    98/139 
  Installing       : libfsverity-1.4-9.fc38.x86_64                       99/139 
  Installing       : zchunk-libs-1.3.1-1.fc38.x86_64                    100/139 
  Installing       : libsolv-0.7.22-4.fc38.x86_64                       101/139 
  Installing       : gnutls-3.8.0-2.fc38.x86_64                         102/139 
  Installing       : glib2-2.76.2-1.fc38.x86_64                         103/139 
  Installing       : libmodulemd-2.15.0-2.fc38.x86_64                   104/139 
  Installing       : libnsl2-2.0.0-5.fc38.x86_64                        105/139 
  Installing       : libssh-0.10.5-1.fc38.x86_64                        106/139 
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  Installing       : python3-3.11.3-1.fc38.x86_64                       108/139 
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  Installing       : python3-dbus-1.3.2-2.fc38.x86_64                   110/139 
  Installing       : python3-libcomps-0.1.18-6.fc38.x86_64              111/139 
  Installing       : python3-distro-1.8.0-2.fc38.noarch                 112/139 
  Installing       : python3-six-1.16.0-9.fc38.noarch                   113/139 
  Installing       : python3-dateutil-1:2.8.2-5.fc38.noarch             114/139 
  Installing       : python3-systemd-235-2.fc38.x86_64                  115/139 
  Installing       : libarchive-3.6.1-4.fc38.x86_64                     116/139 
  Installing       : libevent-2.1.12-8.fc38.x86_64                      117/139 
  Installing       : openldap-2.6.4-1.fc38.x86_64                       118/139 
  Installing       : libcurl-8.0.1-1.fc38.x86_64                        119/139 
  Installing       : gnupg2-2.4.0-3.fc38.x86_64                         120/139 
  Installing       : gpgme-1.17.1-3.fc38.x86_64                         121/139 
  Installing       : librepo-1.15.1-2.fc38.x86_64                       122/139 
  Installing       : libdnf-0.70.0-1.fc38.x86_64                        123/139 
  Installing       : python3-libdnf-0.70.0-1.fc38.x86_64                124/139 
  Installing       : python3-hawkey-0.70.0-1.fc38.x86_64                125/139 
  Installing       : python3-gpg-1.17.1-3.fc38.x86_64                   126/139 
  Running scriptlet: tpm2-tss-4.0.1-3.fc38.x86_64                       127/139 
useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'

  Installing       : tpm2-tss-4.0.1-3.fc38.x86_64                       127/139 
  Installing       : ima-evm-utils-1.4-7.fc38.x86_64                    128/139 
  Installing       : rpm-sign-libs-4.18.1-3.fc38.x86_64                 129/139 
  Installing       : curl-8.0.1-1.fc38.x86_64                           130/139 
  Installing       : elfutils-default-yama-scope-0.189-2.fc38.noarch    131/139 
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  Installing       : elfutils-libs-0.189-2.fc38.x86_64                  132/139 
  Installing       : rpm-build-libs-4.18.1-3.fc38.x86_64                133/139 
  Installing       : python3-rpm-4.18.1-3.fc38.x86_64                   134/139 
  Installing       : python3-dnf-4.15.0-1.fc38.noarch                   135/139 
  Installing       : python3-dnf-plugins-core-4.4.0-1.fc38.noarch       136/139 
  Installing       : dnf-plugins-core-4.4.0-1.fc38.noarch               137/139 
  Installing       : dnf-4.15.0-1.fc38.noarch                           138/139 
  Running scriptlet: dnf-4.15.0-1.fc38.noarch                           138/139 
  Running scriptlet: rpm-4.18.1-3.fc38.x86_64                           139/139 
  Installing       : rpm-4.18.1-3.fc38.x86_64                           139/139 
  Running scriptlet: filesystem-3.18-3.fc38.x86_64                      139/139 
  Running scriptlet: ca-certificates-2023.2.60-2.fc38.noarch            139/139 
  Running scriptlet: rpm-4.18.1-3.fc38.x86_64                           139/139 
  Verifying        : basesystem-11-15.fc38.noarch                         1/139 
  Verifying        : bash-5.2.15-3.fc38.x86_64                            2/139 
  Verifying        : bzip2-libs-1.0.8-13.fc38.x86_64                      3/139 
  Verifying        : ca-certificates-2023.2.60-2.fc38.noarch              4/139 
  Verifying        : crypto-policies-20230301-1.gita12f7b2.fc38.noarc     5/139 
  Verifying        : cyrus-sasl-lib-2.1.28-9.fc38.x86_64                  6/139 
  Verifying        : dbus-libs-1:1.14.6-1.fc38.x86_64                     7/139 
  Verifying        : dnf-plugins-core-4.4.0-1.fc38.noarch                 8/139 
  Verifying        : expat-2.5.0-2.fc38.x86_64                            9/139 
  Verifying        : fedora-gpg-keys-38-1.noarch                         10/139 
  Verifying        : fedora-repos-38-1.noarch                            11/139 
  Verifying        : file-libs-5.44-3.fc38.x86_64                        12/139 
  Verifying        : filesystem-3.18-3.fc38.x86_64                       13/139 
  Verifying        : findutils-1:4.9.0-3.fc38.x86_64                     14/139 
  Verifying        : gawk-5.1.1-5.fc38.x86_64                            15/139 
  Verifying        : gdbm-libs-1:1.23-3.fc38.x86_64                      16/139 
  Verifying        : gmp-1:6.2.1-4.fc38.x86_64                           17/139 
  Verifying        : gnupg2-2.4.0-3.fc38.x86_64                          18/139 
  Verifying        : gnutls-3.8.0-2.fc38.x86_64                          19/139 
  Verifying        : gpgme-1.17.1-3.fc38.x86_64                          20/139 
  Verifying        : grep-3.8-3.fc38.x86_64                              21/139 
  Verifying        : ima-evm-utils-1.4-7.fc38.x86_64                     22/139 
  Verifying        : json-c-0.16-4.fc38.x86_64                           23/139 
  Verifying        : keyutils-libs-1.6.1-6.fc38.x86_64                   24/139 
  Verifying        : krb5-libs-1.20.1-8.fc38.x86_64                      25/139 
  Verifying        : libacl-2.3.1-6.fc38.x86_64                          26/139 
  Verifying        : libarchive-3.6.1-4.fc38.x86_64                      27/139 
  Verifying        : libassuan-2.5.5-6.fc38.x86_64                       28/139 
  Verifying        : libattr-2.5.1-6.fc38.x86_64                         29/139 
  Verifying        : libb2-0.98.1-8.fc38.x86_64                          30/139 
  Verifying        : libblkid-2.38.1-4.fc38.x86_64                       31/139 
  Verifying        : libbrotli-1.0.9-11.fc38.x86_64                      32/139 
  Verifying        : libcap-2.48-6.fc38.x86_64                           33/139 
  Verifying        : libcap-ng-0.8.3-5.fc38.x86_64                       34/139 
  Verifying        : libcom_err-1.46.5-4.fc38.x86_64                     35/139 
  Verifying        : libcomps-0.1.18-6.fc38.x86_64                       36/139 
  Verifying        : libdnf-0.70.0-1.fc38.x86_64                         37/139 
  Verifying        : libeconf-0.4.0-5.fc38.x86_64                        38/139 
  Verifying        : libevent-2.1.12-8.fc38.x86_64                       39/139 
  Verifying        : libffi-3.4.4-2.fc38.x86_64                          40/139 
  Verifying        : libfsverity-1.4-9.fc38.x86_64                       41/139 
  Verifying        : libidn2-2.3.4-2.fc38.x86_64                         42/139 
  Verifying        : libksba-1.6.3-2.fc38.x86_64                         43/139 
  Verifying        : libmount-2.38.1-4.fc38.x86_64                       44/139 
  Verifying        : libnghttp2-1.52.0-1.fc38.x86_64                     45/139 
  Verifying        : libnsl2-2.0.0-5.fc38.x86_64                         46/139 
  Verifying        : libpsl-0.21.2-2.fc38.x86_64                         47/139 
  Verifying        : librepo-1.15.1-2.fc38.x86_64                        48/139 
  Verifying        : libselinux-3.5-1.fc38.x86_64                        49/139 
  Verifying        : libsemanage-3.5-2.fc38.x86_64                       50/139 
  Verifying        : libsepol-3.5-1.fc38.x86_64                          51/139 
  Verifying        : libsigsegv-2.14-4.fc38.x86_64                       52/139 
  Verifying        : libsmartcols-2.38.1-4.fc38.x86_64                   53/139 
  Verifying        : libsolv-0.7.22-4.fc38.x86_64                        54/139 
  Verifying        : libtasn1-4.19.0-2.fc38.x86_64                       55/139 
  Verifying        : libunistring-1.1-3.fc38.x86_64                      56/139 
  Verifying        : libunistring1.0-1.0-1.fc38.x86_64                   57/139 
  Verifying        : libuuid-2.38.1-4.fc38.x86_64                        58/139 
  Verifying        : libverto-0.3.2-5.fc38.x86_64                        59/139 
  Verifying        : libxcrypt-4.4.33-7.fc38.x86_64                      60/139 
  Verifying        : libyaml-0.2.5-9.fc38.x86_64                         61/139 
  Verifying        : lua-libs-5.4.4-9.fc38.x86_64                        62/139 
  Verifying        : lz4-libs-1.9.4-2.fc38.x86_64                        63/139 
  Verifying        : mpdecimal-2.5.1-6.fc38.x86_64                       64/139 
  Verifying        : mpfr-4.1.1-3.fc38.x86_64                            65/139 
  Verifying        : ncurses-base-6.4-3.20230114.fc38.noarch             66/139 
  Verifying        : ncurses-libs-6.4-3.20230114.fc38.x86_64             67/139 
  Verifying        : nettle-3.8-3.fc38.x86_64                            68/139 
  Verifying        : npth-1.6-12.fc38.x86_64                             69/139 
  Verifying        : openldap-2.6.4-1.fc38.x86_64                        70/139 
  Verifying        : openssl-libs-1:3.0.8-2.fc38.x86_64                  71/139 
  Verifying        : p11-kit-0.24.1-6.fc38.x86_64                        72/139 
  Verifying        : p11-kit-trust-0.24.1-6.fc38.x86_64                  73/139 
  Verifying        : pcre2-10.42-1.fc38.1.x86_64                         74/139 
  Verifying        : pcre2-syntax-10.42-1.fc38.1.noarch                  75/139 
  Verifying        : popt-1.19-2.fc38.x86_64                             76/139 
  Verifying        : publicsuffix-list-dafsa-20230318-1.fc38.noarch      77/139 
  Verifying        : python-pip-wheel-22.3.1-2.fc38.noarch               78/139 
  Verifying        : python-setuptools-wheel-65.5.1-2.fc38.noarch        79/139 
  Verifying        : python3-dateutil-1:2.8.2-5.fc38.noarch              80/139 
  Verifying        : python3-dbus-1.3.2-2.fc38.x86_64                    81/139 
  Verifying        : python3-distro-1.8.0-2.fc38.noarch                  82/139 
  Verifying        : python3-dnf-plugins-core-4.4.0-1.fc38.noarch        83/139 
  Verifying        : python3-gpg-1.17.1-3.fc38.x86_64                    84/139 
  Verifying        : python3-hawkey-0.70.0-1.fc38.x86_64                 85/139 
  Verifying        : python3-libcomps-0.1.18-6.fc38.x86_64               86/139 
  Verifying        : python3-libdnf-0.70.0-1.fc38.x86_64                 87/139 
  Verifying        : python3-six-1.16.0-9.fc38.noarch                    88/139 
  Verifying        : python3-systemd-235-2.fc38.x86_64                   89/139 
  Verifying        : readline-8.2-3.fc38.x86_64                          90/139 
  Verifying        : sed-4.8-12.fc38.x86_64                              91/139 
  Verifying        : setup-2.14.3-2.fc38.noarch                          92/139 
  Verifying        : shadow-utils-2:4.13-6.fc38.x86_64                   93/139 
  Verifying        : sqlite-libs-3.40.1-2.fc38.x86_64                    94/139 
  Verifying        : tpm2-tss-4.0.1-3.fc38.x86_64                        95/139 
  Verifying        : tzdata-2023c-1.fc38.noarch                          96/139 
  Verifying        : xz-libs-5.4.1-1.fc38.x86_64                         97/139 
  Verifying        : zlib-1.2.13-3.fc38.x86_64                           98/139 
  Verifying        : alternatives-1.24-1.fc38.x86_64                     99/139 
  Verifying        : audit-libs-3.1.1-1.fc38.x86_64                     100/139 
  Verifying        : coreutils-9.1-12.fc38.x86_64                       101/139 
  Verifying        : coreutils-common-9.1-12.fc38.x86_64                102/139 
  Verifying        : curl-8.0.1-1.fc38.x86_64                           103/139 
  Verifying        : dnf-4.15.0-1.fc38.noarch                           104/139 
  Verifying        : dnf-data-4.15.0-1.fc38.noarch                      105/139 
  Verifying        : elfutils-default-yama-scope-0.189-2.fc38.noarch    106/139 
  Verifying        : elfutils-libelf-0.189-2.fc38.x86_64                107/139 
  Verifying        : elfutils-libs-0.189-2.fc38.x86_64                  108/139 
  Verifying        : fedora-release-38-35.noarch                        109/139 
  Verifying        : fedora-release-common-38-35.noarch                 110/139 
  Verifying        : fedora-release-identity-basic-38-35.noarch         111/139 
  Verifying        : glib2-2.76.2-1.fc38.x86_64                         112/139 
  Verifying        : glibc-2.37-4.fc38.x86_64                           113/139 
  Verifying        : glibc-common-2.37-4.fc38.x86_64                    114/139 
  Verifying        : glibc-minimal-langpack-2.37-4.fc38.x86_64          115/139 
  Verifying        : libcurl-8.0.1-1.fc38.x86_64                        116/139 
  Verifying        : libgcc-13.1.1-2.fc38.x86_64                        117/139 
  Verifying        : libgcrypt-1.10.2-1.fc38.x86_64                     118/139 
  Verifying        : libgomp-13.1.1-2.fc38.x86_64                       119/139 
  Verifying        : libgpg-error-1.47-1.fc38.x86_64                    120/139 
  Verifying        : libmodulemd-2.15.0-2.fc38.x86_64                   121/139 
  Verifying        : libreport-filesystem-2.17.10-1.fc38.noarch         122/139 
  Verifying        : libssh-0.10.5-1.fc38.x86_64                        123/139 
  Verifying        : libssh-config-0.10.5-1.fc38.noarch                 124/139 
  Verifying        : libstdc++-13.1.1-2.fc38.x86_64                     125/139 
  Verifying        : libtirpc-1.3.3-1.rc1.fc38.x86_64                   126/139 
  Verifying        : libxml2-2.10.4-1.fc38.x86_64                       127/139 
  Verifying        : libzstd-1.5.5-1.fc38.x86_64                        128/139 
  Verifying        : python3-3.11.3-1.fc38.x86_64                       129/139 
  Verifying        : python3-dnf-4.15.0-1.fc38.noarch                   130/139 
  Verifying        : python3-libs-3.11.3-1.fc38.x86_64                  131/139 
  Verifying        : python3-rpm-4.18.1-3.fc38.x86_64                   132/139 
  Verifying        : rpm-4.18.1-3.fc38.x86_64                           133/139 
  Verifying        : rpm-build-libs-4.18.1-3.fc38.x86_64                134/139 
  Verifying        : rpm-libs-4.18.1-3.fc38.x86_64                      135/139 
  Verifying        : rpm-sequoia-1.4.0-2.fc38.x86_64                    136/139 
  Verifying        : rpm-sign-libs-4.18.1-3.fc38.x86_64                 137/139 
  Verifying        : systemd-libs-253.4-1.fc38.x86_64                   138/139 
  Verifying        : zchunk-libs-1.3.1-1.fc38.x86_64                    139/139 
Installed products updated.

Installed:
  alternatives-1.24-1.fc38.x86_64                                               
  audit-libs-3.1.1-1.fc38.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-9.1-12.fc38.x86_64                                                  
  coreutils-common-9.1-12.fc38.x86_64                                           
  crypto-policies-20230301-1.gita12f7b2.fc38.noarch                             
  curl-8.0.1-1.fc38.x86_64                                                      
  cyrus-sasl-lib-2.1.28-9.fc38.x86_64                                           
  dbus-libs-1:1.14.6-1.fc38.x86_64                                              
  dnf-4.15.0-1.fc38.noarch                                                      
  dnf-data-4.15.0-1.fc38.noarch                                                 
  dnf-plugins-core-4.4.0-1.fc38.noarch                                          
  elfutils-default-yama-scope-0.189-2.fc38.noarch                               
  elfutils-libelf-0.189-2.fc38.x86_64                                           
  elfutils-libs-0.189-2.fc38.x86_64                                             
  expat-2.5.0-2.fc38.x86_64                                                     
  fedora-gpg-keys-38-1.noarch                                                   
  fedora-release-38-35.noarch                                                   
  fedora-release-common-38-35.noarch                                            
  fedora-release-identity-basic-38-35.noarch                                    
  fedora-repos-38-1.noarch                                                      
  file-libs-5.44-3.fc38.x86_64                                                  
  filesystem-3.18-3.fc38.x86_64                                                 
  findutils-1:4.9.0-3.fc38.x86_64                                               
  gawk-5.1.1-5.fc38.x86_64                                                      
  gdbm-libs-1:1.23-3.fc38.x86_64                                                
  glib2-2.76.2-1.fc38.x86_64                                                    
  glibc-2.37-4.fc38.x86_64                                                      
  glibc-common-2.37-4.fc38.x86_64                                               
  glibc-minimal-langpack-2.37-4.fc38.x86_64                                     
  gmp-1:6.2.1-4.fc38.x86_64                                                     
  gnupg2-2.4.0-3.fc38.x86_64                                                    
  gnutls-3.8.0-2.fc38.x86_64                                                    
  gpgme-1.17.1-3.fc38.x86_64                                                    
  grep-3.8-3.fc38.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-1.20.1-8.fc38.x86_64                                                
  libacl-2.3.1-6.fc38.x86_64                                                    
  libarchive-3.6.1-4.fc38.x86_64                                                
  libassuan-2.5.5-6.fc38.x86_64                                                 
  libattr-2.5.1-6.fc38.x86_64                                                   
  libb2-0.98.1-8.fc38.x86_64                                                    
  libblkid-2.38.1-4.fc38.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-0.1.18-6.fc38.x86_64                                                 
  libcurl-8.0.1-1.fc38.x86_64                                                   
  libdnf-0.70.0-1.fc38.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.fc38.x86_64                                                   
  libgcrypt-1.10.2-1.fc38.x86_64                                                
  libgomp-13.1.1-2.fc38.x86_64                                                  
  libgpg-error-1.47-1.fc38.x86_64                                               
  libidn2-2.3.4-2.fc38.x86_64                                                   
  libksba-1.6.3-2.fc38.x86_64                                                   
  libmodulemd-2.15.0-2.fc38.x86_64                                              
  libmount-2.38.1-4.fc38.x86_64                                                 
  libnghttp2-1.52.0-1.fc38.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.fc38.noarch                                    
  libselinux-3.5-1.fc38.x86_64                                                  
  libsemanage-3.5-2.fc38.x86_64                                                 
  libsepol-3.5-1.fc38.x86_64                                                    
  libsigsegv-2.14-4.fc38.x86_64                                                 
  libsmartcols-2.38.1-4.fc38.x86_64                                             
  libsolv-0.7.22-4.fc38.x86_64                                                  
  libssh-0.10.5-1.fc38.x86_64                                                   
  libssh-config-0.10.5-1.fc38.noarch                                            
  libstdc++-13.1.1-2.fc38.x86_64                                                
  libtasn1-4.19.0-2.fc38.x86_64                                                 
  libtirpc-1.3.3-1.rc1.fc38.x86_64                                              
  libunistring-1.1-3.fc38.x86_64                                                
  libunistring1.0-1.0-1.fc38.x86_64                                             
  libuuid-2.38.1-4.fc38.x86_64                                                  
  libverto-0.3.2-5.fc38.x86_64                                                  
  libxcrypt-4.4.33-7.fc38.x86_64                                                
  libxml2-2.10.4-1.fc38.x86_64                                                  
  libyaml-0.2.5-9.fc38.x86_64                                                   
  libzstd-1.5.5-1.fc38.x86_64                                                   
  lua-libs-5.4.4-9.fc38.x86_64                                                  
  lz4-libs-1.9.4-2.fc38.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-2.6.4-1.fc38.x86_64                                                  
  openssl-libs-1:3.0.8-2.fc38.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.fc38.noarch                                
  python-pip-wheel-22.3.1-2.fc38.noarch                                         
  python-setuptools-wheel-65.5.1-2.fc38.noarch                                  
  python3-3.11.3-1.fc38.x86_64                                                  
  python3-dateutil-1:2.8.2-5.fc38.noarch                                        
  python3-dbus-1.3.2-2.fc38.x86_64                                              
  python3-distro-1.8.0-2.fc38.noarch                                            
  python3-dnf-4.15.0-1.fc38.noarch                                              
  python3-dnf-plugins-core-4.4.0-1.fc38.noarch                                  
  python3-gpg-1.17.1-3.fc38.x86_64                                              
  python3-hawkey-0.70.0-1.fc38.x86_64                                           
  python3-libcomps-0.1.18-6.fc38.x86_64                                         
  python3-libdnf-0.70.0-1.fc38.x86_64                                           
  python3-libs-3.11.3-1.fc38.x86_64                                             
  python3-rpm-4.18.1-3.fc38.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.fc38.x86_64                                                      
  rpm-build-libs-4.18.1-3.fc38.x86_64                                           
  rpm-libs-4.18.1-3.fc38.x86_64                                                 
  rpm-sequoia-1.4.0-2.fc38.x86_64                                               
  rpm-sign-libs-4.18.1-3.fc38.x86_64                                            
  sed-4.8-12.fc38.x86_64                                                        
  setup-2.14.3-2.fc38.noarch                                                    
  shadow-utils-2:4.13-6.fc38.x86_64                                             
  sqlite-libs-3.40.1-2.fc38.x86_64                                              
  systemd-libs-253.4-1.fc38.x86_64                                              
  tpm2-tss-4.0.1-3.fc38.x86_64                                                  
  tzdata-2023c-1.fc38.noarch                                                    
  xz-libs-5.4.1-1.fc38.x86_64                                                   
  zchunk-libs-1.3.1-1.fc38.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-38-x86_64-1684275155.629876/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                                 2.3 kB/s | 257  B     00:00    
fedora                                           19 MB/s |  83 MB     00:04    
updates                                          14 MB/s |  17 MB     00:01    
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 9.1-12.fc38                 updates 1.1 M
 cpio                          x86_64 2.13-14.fc38                fedora  276 k
 diffutils                     x86_64 3.9-1.fc38                  fedora  397 k
 fedora-release-common         noarch 38-35                       updates  22 k
 findutils                     x86_64 1:4.9.0-3.fc38              fedora  492 k
 gawk                          x86_64 5.1.1-5.fc38                fedora  1.0 M
 glibc-minimal-langpack        x86_64 2.37-4.fc38                 updates  37 k
 grep                          x86_64 3.8-3.fc38                  fedora  293 k
 gzip                          x86_64 1.12-3.fc38                 fedora  166 k
 info                          x86_64 7.0.2-2.fc38                fedora  181 k
 patch                         x86_64 2.7.6-19.fc38               fedora  126 k
 redhat-rpm-config             noarch 252-1.fc38                  fedora   83 k
 rpm-build                     x86_64 4.18.1-3.fc38               updates  77 k
 sed                           x86_64 4.8-12.fc38                 fedora  306 k
 shadow-utils                  x86_64 2:4.13-6.fc38               fedora  1.3 M
 tar                           x86_64 2:1.34-8.fc38               fedora  889 k
 unzip                         x86_64 6.0-60.fc38                 fedora  184 k
 util-linux                    x86_64 2.38.1-4.fc38               fedora  2.3 M
 which                         x86_64 2.21-39.fc38                fedora   42 k
 xz                            x86_64 5.4.1-1.fc38                fedora  419 k
Installing dependencies:
 alternatives                  x86_64 1.24-1.fc38                 updates  39 k
 ansible-srpm-macros           noarch 1-9.1.fc38                  fedora  8.8 k
 audit-libs                    x86_64 3.1.1-1.fc38                updates 116 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 2.39-9.fc38                 fedora  5.4 M
 binutils-gold                 x86_64 2.39-9.fc38                 fedora  784 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 9.1-12.fc38                 updates 2.0 M
 cracklib                      x86_64 2.9.7-31.fc38               fedora   92 k
 crypto-policies               noarch 20230301-1.gita12f7b2.fc38  fedora   93 k
 curl                          x86_64 8.0.1-1.fc38                updates 350 k
 cyrus-sasl-lib                x86_64 2.1.28-9.fc38               fedora  794 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.fc38                updates 536 k
 elfutils-debuginfod-client    x86_64 0.189-2.fc38                updates  39 k
 elfutils-default-yama-scope   noarch 0.189-2.fc38                updates  15 k
 elfutils-libelf               x86_64 0.189-2.fc38                updates 196 k
 elfutils-libs                 x86_64 0.189-2.fc38                updates 260 k
 fedora-gpg-keys               noarch 38-1                        fedora  126 k
 fedora-release                noarch 38-35                       updates  12 k
 fedora-release-identity-basic noarch 38-35                       updates  13 k
 fedora-repos                  noarch 38-1                        fedora  9.1 k
 file                          x86_64 5.44-3.fc38                 fedora   49 k
 file-libs                     x86_64 5.44-3.fc38                 fedora  730 k
 filesystem                    x86_64 3.18-3.fc38                 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 13.1-4.fc38                 updates 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 2.37-4.fc38                 updates 2.1 M
 glibc-common                  x86_64 2.37-4.fc38                 updates 314 k
 glibc-gconv-extra             x86_64 2.37-4.fc38                 updates 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 3.2.0-2.fc38                fedora   27 k
 jansson                       x86_64 2.13.1-6.fc38               fedora   44 k
 kernel-srpm-macros            noarch 1.0-16.fc38                 fedora  9.3 k
 keyutils-libs                 x86_64 1.6.1-6.fc38                fedora   31 k
 krb5-libs                     x86_64 1.20.1-8.fc38               fedora  727 k
 libacl                        x86_64 2.3.1-6.fc38                fedora   23 k
 libarchive                    x86_64 3.6.1-4.fc38                fedora  400 k
 libattr                       x86_64 2.5.1-6.fc38                fedora   18 k
 libblkid                      x86_64 2.38.1-4.fc38               fedora  106 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 8.0.1-1.fc38                updates 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 2.38.1-4.fc38               fedora  161 k
 libffi                        x86_64 3.4.4-2.fc38                fedora   38 k
 libgcc                        x86_64 13.1.1-2.fc38               updates 106 k
 libgomp                       x86_64 13.1.1-2.fc38               updates 316 k
 libidn2                       x86_64 2.3.4-2.fc38                fedora  160 k
 libmount                      x86_64 2.38.1-4.fc38               fedora  135 k
 libnghttp2                    x86_64 1.52.0-1.fc38               fedora   75 k
 libnsl2                       x86_64 2.0.0-5.fc38                fedora   30 k
 libpkgconf                    x86_64 1.8.0-6.fc38                fedora   35 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.fc38                  fedora   87 k
 libsemanage                   x86_64 3.5-2.fc38                  fedora  120 k
 libsepol                      x86_64 3.5-1.fc38                  fedora  324 k
 libsigsegv                    x86_64 2.14-4.fc38                 fedora   27 k
 libsmartcols                  x86_64 2.38.1-4.fc38               fedora   64 k
 libssh                        x86_64 0.10.5-1.fc38               updates 211 k
 libssh-config                 noarch 0.10.5-1.fc38               updates 9.0 k
 libstdc++                     x86_64 13.1.1-2.fc38               updates 860 k
 libtasn1                      x86_64 4.19.0-2.fc38               fedora   74 k
 libtirpc                      x86_64 1.3.3-1.rc1.fc38            updates  93 k
 libunistring1.0               x86_64 1.0-1.fc38                  fedora  539 k
 libutempter                   x86_64 1.2.1-8.fc38                fedora   26 k
 libuuid                       x86_64 2.38.1-4.fc38               fedora   28 k
 libverto                      x86_64 0.3.2-5.fc38                fedora   21 k
 libxcrypt                     x86_64 4.4.33-7.fc38               fedora  120 k
 libxml2                       x86_64 2.10.4-1.fc38               updates 701 k
 libzstd                       x86_64 1.5.5-1.fc38                updates 308 k
 lua-libs                      x86_64 5.4.4-9.fc38                fedora  133 k
 lua-srpm-macros               noarch 1-8.fc38                    fedora  8.6 k
 lz4-libs                      x86_64 1.9.4-2.fc38                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 2.6.4-1.fc38                fedora  254 k
 openssl-libs                  x86_64 1:3.0.8-2.fc38              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 1.5.2-16.fc38               fedora  560 k
 pam-libs                      x86_64 1.5.2-16.fc38               fedora   58 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 1.8.0-6.fc38                fedora   41 k
 pkgconf-m4                    noarch 1.8.0-6.fc38                fedora   14 k
 pkgconf-pkg-config            x86_64 1.8.0-6.fc38                fedora  9.6 k
 popt                          x86_64 1.19-2.fc38                 fedora   67 k
 publicsuffix-list-dafsa       noarch 20230318-1.fc38             fedora   60 k
 pyproject-srpm-macros         noarch 1.7.0-1.fc38                updates  14 k
 python-srpm-macros            noarch 3.11-10.fc38                fedora   26 k
 qt5-srpm-macros               noarch 5.15.9-1.fc38               updates 8.1 k
 readline                      x86_64 8.2-3.fc38                  fedora  212 k
 rpm                           x86_64 4.18.1-3.fc38               updates 570 k
 rpm-build-libs                x86_64 4.18.1-3.fc38               updates  94 k
 rpm-libs                      x86_64 4.18.1-3.fc38               updates 313 k
 rpm-sequoia                   x86_64 1.4.0-2.fc38                updates 850 k
 rpmautospec-rpm-macros        noarch 0.3.5-1.fc38                fedora  9.3 k
 rust-srpm-macros              noarch 24-1.fc38                   fedora   12 k
 setup                         noarch 2.14.3-2.fc38               fedora  152 k
 sqlite-libs                   x86_64 3.40.1-2.fc38               fedora  666 k
 systemd-libs                  x86_64 253.4-1.fc38                updates 652 k
 tzdata                        noarch 2023c-1.fc38                fedora  718 k
 util-linux-core               x86_64 2.38.1-4.fc38               fedora  473 k
 xxhash-libs                   x86_64 0.8.1-4.fc38                fedora   40 k
 xz-libs                       x86_64 5.4.1-1.fc38                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.fc38                updates 482 k
Installing Groups:
 Buildsystem building group                                                    

Transaction Summary
================================================================================
Install  151 Packages

Total download size: 53 M
Installed size: 183 M
Downloading Packages:
(1/151): ansible-srpm-macros-1-9.1.fc38.noarch.  61 kB/s | 8.8 kB     00:00    
(2/151): basesystem-11-15.fc38.noarch.rpm        99 kB/s | 7.0 kB     00:00    
(3/151): authselect-1.4.2-2.fc38.x86_64.rpm     407 kB/s | 144 kB     00:00    
(4/151): authselect-libs-1.4.2-2.fc38.x86_64.rp 579 kB/s | 249 kB     00:00    
(5/151): binutils-gold-2.39-9.fc38.x86_64.rpm   3.5 MB/s | 784 kB     00:00    
(6/151): bzip2-1.0.8-13.fc38.x86_64.rpm         691 kB/s |  52 kB     00:00    
(7/151): bash-5.2.15-3.fc38.x86_64.rpm          3.5 MB/s | 1.8 MB     00:00    
(8/151): binutils-2.39-9.fc38.x86_64.rpm         12 MB/s | 5.4 MB     00:00    
(9/151): bzip2-libs-1.0.8-13.fc38.x86_64.rpm    573 kB/s |  41 kB     00:00    
(10/151): ca-certificates-2023.2.60-2.fc38.noar 9.8 MB/s | 845 kB     00:00    
(11/151): cpio-2.13-14.fc38.x86_64.rpm          3.7 MB/s | 276 kB     00:00    
(12/151): cracklib-2.9.7-31.fc38.x86_64.rpm     1.2 MB/s |  92 kB     00:00    
(13/151): crypto-policies-20230301-1.gita12f7b2 1.3 MB/s |  93 kB     00:00    
(14/151): cyrus-sasl-lib-2.1.28-9.fc38.x86_64.r 9.9 MB/s | 794 kB     00:00    
(15/151): debugedit-5.0-7.fc38.x86_64.rpm       1.0 MB/s |  78 kB     00:00    
(16/151): diffutils-3.9-1.fc38.x86_64.rpm       5.1 MB/s | 397 kB     00:00    
(17/151): dwz-0.15-2.fc38.x86_64.rpm            1.8 MB/s | 135 kB     00:00    
(18/151): ed-1.19-2.fc38.x86_64.rpm             1.1 MB/s |  78 kB     00:00    
(19/151): efi-srpm-macros-5-7.fc38.noarch.rpm   312 kB/s |  22 kB     00:00    
(20/151): fedora-gpg-keys-38-1.noarch.rpm       1.7 MB/s | 126 kB     00:00    
(21/151): fedora-repos-38-1.noarch.rpm          127 kB/s | 9.1 kB     00:00    
(22/151): file-5.44-3.fc38.x86_64.rpm           691 kB/s |  49 kB     00:00    
(23/151): file-libs-5.44-3.fc38.x86_64.rpm      9.1 MB/s | 730 kB     00:00    
(24/151): findutils-4.9.0-3.fc38.x86_64.rpm     6.3 MB/s | 492 kB     00:00    
(25/151): fonts-srpm-macros-2.0.5-11.fc38.noarc 371 kB/s |  26 kB     00:00    
(26/151): filesystem-3.18-3.fc38.x86_64.rpm     7.2 MB/s | 1.1 MB     00:00    
(27/151): fpc-srpm-macros-1.3-7.fc38.noarch.rpm 109 kB/s | 7.8 kB     00:00    
(28/151): gdbm-libs-1.23-3.fc38.x86_64.rpm      715 kB/s |  56 kB     00:00    
(29/151): ghc-srpm-macros-1.6.1-1.fc38.noarch.r 112 kB/s | 8.0 kB     00:00    
(30/151): gmp-6.2.1-4.fc38.x86_64.rpm           4.1 MB/s | 313 kB     00:00    
(31/151): gnat-srpm-macros-6-2.fc38.noarch.rpm  124 kB/s | 8.8 kB     00:00    
(32/151): go-srpm-macros-3.2.0-2.fc38.noarch.rp 375 kB/s |  27 kB     00:00    
(33/151): grep-3.8-3.fc38.x86_64.rpm            3.8 MB/s | 293 kB     00:00    
(34/151): gzip-1.12-3.fc38.x86_64.rpm           2.2 MB/s | 166 kB     00:00    
(35/151): info-7.0.2-2.fc38.x86_64.rpm          2.4 MB/s | 181 kB     00:00    
(36/151): jansson-2.13.1-6.fc38.x86_64.rpm      611 kB/s |  44 kB     00:00    
(37/151): kernel-srpm-macros-1.0-16.fc38.noarch 131 kB/s | 9.3 kB     00:00    
(38/151): keyutils-libs-1.6.1-6.fc38.x86_64.rpm 431 kB/s |  31 kB     00:00    
(39/151): krb5-libs-1.20.1-8.fc38.x86_64.rpm    8.6 MB/s | 727 kB     00:00    
(40/151): libacl-2.3.1-6.fc38.x86_64.rpm        319 kB/s |  23 kB     00:00    
(41/151): gawk-5.1.1-5.fc38.x86_64.rpm          1.9 MB/s | 1.0 MB     00:00    
(42/151): libarchive-3.6.1-4.fc38.x86_64.rpm    5.0 MB/s | 400 kB     00:00    
(43/151): libattr-2.5.1-6.fc38.x86_64.rpm       250 kB/s |  18 kB     00:00    
(44/151): libblkid-2.38.1-4.fc38.x86_64.rpm     1.4 MB/s | 106 kB     00:00    
(45/151): libbrotli-1.0.9-11.fc38.x86_64.rpm    4.2 MB/s | 317 kB     00:00    
(46/151): libcap-2.48-6.fc38.x86_64.rpm         923 kB/s |  67 kB     00:00    
(47/151): libcap-ng-0.8.3-5.fc38.x86_64.rpm     454 kB/s |  32 kB     00:00    
(48/151): libcom_err-1.46.5-4.fc38.x86_64.rpm   359 kB/s |  26 kB     00:00    
(49/151): libdb-5.3.28-55.fc38.x86_64.rpm       9.3 MB/s | 758 kB     00:00    
(50/151): libeconf-0.4.0-5.fc38.x86_64.rpm      379 kB/s |  27 kB     00:00    
(51/151): libevent-2.1.12-8.fc38.x86_64.rpm     3.4 MB/s | 257 kB     00:00    
(52/151): libfdisk-2.38.1-4.fc38.x86_64.rpm     2.1 MB/s | 161 kB     00:00    
(53/151): libffi-3.4.4-2.fc38.x86_64.rpm        530 kB/s |  38 kB     00:00    
(54/151): libidn2-2.3.4-2.fc38.x86_64.rpm       2.1 MB/s | 160 kB     00:00    
(55/151): libmount-2.38.1-4.fc38.x86_64.rpm     1.8 MB/s | 135 kB     00:00    
(56/151): libnghttp2-1.52.0-1.fc38.x86_64.rpm   1.0 MB/s |  75 kB     00:00    
(57/151): libnsl2-2.0.0-5.fc38.x86_64.rpm       418 kB/s |  30 kB     00:00    
(58/151): libpkgconf-1.8.0-6.fc38.x86_64.rpm    492 kB/s |  35 kB     00:00    
(59/151): libpsl-0.21.2-2.fc38.x86_64.rpm       900 kB/s |  65 kB     00:00    
(60/151): libpwquality-1.4.5-3.fc38.x86_64.rpm  1.6 MB/s | 119 kB     00:00    
(61/151): libselinux-3.5-1.fc38.x86_64.rpm      1.2 MB/s |  87 kB     00:00    
(62/151): libsemanage-3.5-2.fc38.x86_64.rpm     1.6 MB/s | 120 kB     00:00    
(63/151): libsepol-3.5-1.fc38.x86_64.rpm        4.2 MB/s | 324 kB     00:00    
(64/151): libsigsegv-2.14-4.fc38.x86_64.rpm     376 kB/s |  27 kB     00:00    
(65/151): libsmartcols-2.38.1-4.fc38.x86_64.rpm 889 kB/s |  64 kB     00:00    
(66/151): libtasn1-4.19.0-2.fc38.x86_64.rpm     1.0 MB/s |  74 kB     00:00    
(67/151): libunistring1.0-1.0-1.fc38.x86_64.rpm 6.9 MB/s | 539 kB     00:00    
(68/151): libutempter-1.2.1-8.fc38.x86_64.rpm   359 kB/s |  26 kB     00:00    
(69/151): libuuid-2.38.1-4.fc38.x86_64.rpm      387 kB/s |  28 kB     00:00    
(70/151): libverto-0.3.2-5.fc38.x86_64.rpm      291 kB/s |  21 kB     00:00    
(71/151): libxcrypt-4.4.33-7.fc38.x86_64.rpm    1.6 MB/s | 120 kB     00:00    
(72/151): lua-libs-5.4.4-9.fc38.x86_64.rpm      1.8 MB/s | 133 kB     00:00    
(73/151): lua-srpm-macros-1-8.fc38.noarch.rpm   119 kB/s | 8.6 kB     00:00    
(74/151): lz4-libs-1.9.4-2.fc38.x86_64.rpm      921 kB/s |  67 kB     00:00    
(75/151): mpfr-4.1.1-3.fc38.x86_64.rpm          7.4 MB/s | 600 kB     00:00    
(76/151): ncurses-base-6.4-3.20230114.fc38.noar 1.2 MB/s |  87 kB     00:00    
(77/151): ncurses-libs-6.4-3.20230114.fc38.x86_ 4.3 MB/s | 333 kB     00:00    
(78/151): ocaml-srpm-macros-7-3.fc38.noarch.rpm 188 kB/s |  13 kB     00:00    
(79/151): openblas-srpm-macros-2-13.fc38.noarch 106 kB/s | 7.5 kB     00:00    
(80/151): openldap-2.6.4-1.fc38.x86_64.rpm      3.3 MB/s | 254 kB     00:00    
(81/151): p11-kit-0.24.1-6.fc38.x86_64.rpm      4.2 MB/s | 359 kB     00:00    
(82/151): p11-kit-trust-0.24.1-6.fc38.x86_64.rp 1.7 MB/s | 136 kB     00:00    
(83/151): package-notes-srpm-macros-0.5-7.fc38. 125 kB/s |  11 kB     00:00    
(84/151): pam-1.5.2-16.fc38.x86_64.rpm          5.5 MB/s | 560 kB     00:00    
(85/151): openssl-libs-3.0.8-2.fc38.x86_64.rpm  8.9 MB/s | 2.1 MB     00:00    
(86/151): pam-libs-1.5.2-16.fc38.x86_64.rpm     806 kB/s |  58 kB     00:00    
(87/151): patch-2.7.6-19.fc38.x86_64.rpm        1.7 MB/s | 126 kB     00:00    
(88/151): pcre2-10.42-1.fc38.1.x86_64.rpm       3.1 MB/s | 234 kB     00:00    
(89/151): pcre2-syntax-10.42-1.fc38.1.noarch.rp 1.9 MB/s | 144 kB     00:00    
(90/151): perl-srpm-macros-1-48.fc38.noarch.rpm 116 kB/s | 8.4 kB     00:00    
(91/151): pkgconf-1.8.0-6.fc38.x86_64.rpm       567 kB/s |  41 kB     00:00    
(92/151): pkgconf-m4-1.8.0-6.fc38.noarch.rpm    195 kB/s |  14 kB     00:00    
(93/151): pkgconf-pkg-config-1.8.0-6.fc38.x86_6 130 kB/s | 9.6 kB     00:00    
(94/151): popt-1.19-2.fc38.x86_64.rpm           924 kB/s |  67 kB     00:00    
(95/151): publicsuffix-list-dafsa-20230318-1.fc 840 kB/s |  60 kB     00:00    
(96/151): python-srpm-macros-3.11-10.fc38.noarc 358 kB/s |  26 kB     00:00    
(97/151): readline-8.2-3.fc38.x86_64.rpm        2.8 MB/s | 212 kB     00:00    
(98/151): redhat-rpm-config-252-1.fc38.noarch.r 1.1 MB/s |  83 kB     00:00    
(99/151): rpmautospec-rpm-macros-0.3.5-1.fc38.n 129 kB/s | 9.3 kB     00:00    
(100/151): rust-srpm-macros-24-1.fc38.noarch.rp 172 kB/s |  12 kB     00:00    
(101/151): sed-4.8-12.fc38.x86_64.rpm           4.1 MB/s | 306 kB     00:00    
(102/151): setup-2.14.3-2.fc38.noarch.rpm       2.0 MB/s | 152 kB     00:00    
(103/151): sqlite-libs-3.40.1-2.fc38.x86_64.rpm 8.4 MB/s | 666 kB     00:00    
(104/151): tar-1.34-8.fc38.x86_64.rpm            11 MB/s | 889 kB     00:00    
(105/151): tzdata-2023c-1.fc38.noarch.rpm       8.9 MB/s | 718 kB     00:00    
(106/151): unzip-6.0-60.fc38.x86_64.rpm         2.4 MB/s | 184 kB     00:00    
(107/151): util-linux-core-2.38.1-4.fc38.x86_64 6.0 MB/s | 473 kB     00:00    
(108/151): which-2.21-39.fc38.x86_64.rpm        583 kB/s |  42 kB     00:00    
(109/151): util-linux-2.38.1-4.fc38.x86_64.rpm   10 MB/s | 2.3 MB     00:00    
(110/151): xxhash-libs-0.8.1-4.fc38.x86_64.rpm  556 kB/s |  40 kB     00:00    
(111/151): xz-5.4.1-1.fc38.x86_64.rpm           5.5 MB/s | 419 kB     00:00    
(112/151): xz-libs-5.4.1-1.fc38.x86_64.rpm      1.4 MB/s | 108 kB     00:00    
(113/151): zip-3.0-36.fc38.x86_64.rpm           3.5 MB/s | 265 kB     00:00    
(114/151): zlib-1.2.13-3.fc38.x86_64.rpm        1.3 MB/s |  95 kB     00:00    
(115/151): alternatives-1.24-1.fc38.x86_64.rpm  662 kB/s |  39 kB     00:00    
(116/151): audit-libs-3.1.1-1.fc38.x86_64.rpm   1.3 MB/s | 116 kB     00:00    
(117/151): coreutils-9.1-12.fc38.x86_64.rpm      10 MB/s | 1.1 MB     00:00    
(118/151): shadow-utils-4.13-6.fc38.x86_64.rpm  1.7 MB/s | 1.3 MB     00:00    
(119/151): coreutils-common-9.1-12.fc38.x86_64.  20 MB/s | 2.0 MB     00:00    
(120/151): curl-8.0.1-1.fc38.x86_64.rpm          11 MB/s | 350 kB     00:00    
(121/151): elfutils-debuginfod-client-0.189-2.f 2.3 MB/s |  39 kB     00:00    
(122/151): elfutils-default-yama-scope-0.189-2. 910 kB/s |  15 kB     00:00    
(123/151): elfutils-libelf-0.189-2.fc38.x86_64. 7.5 MB/s | 196 kB     00:00    
(124/151): elfutils-libs-0.189-2.fc38.x86_64.rp 9.8 MB/s | 260 kB     00:00    
(125/151): fedora-release-38-35.noarch.rpm      683 kB/s |  12 kB     00:00    
(126/151): fedora-release-common-38-35.noarch.r 1.2 MB/s |  22 kB     00:00    
(127/151): fedora-release-identity-basic-38-35. 803 kB/s |  13 kB     00:00    
(128/151): glibc-2.37-4.fc38.x86_64.rpm          20 MB/s | 2.1 MB     00:00    
(129/151): gdb-minimal-13.1-4.fc38.x86_64.rpm    32 MB/s | 4.2 MB     00:00    
(130/151): elfutils-0.189-2.fc38.x86_64.rpm     2.3 MB/s | 536 kB     00:00    
(131/151): glibc-common-2.37-4.fc38.x86_64.rpm   15 MB/s | 314 kB     00:00    
(132/151): glibc-gconv-extra-2.37-4.fc38.x86_64  43 MB/s | 1.6 MB     00:00    
(133/151): glibc-minimal-langpack-2.37-4.fc38.x 1.1 MB/s |  37 kB     00:00    
(134/151): libcurl-8.0.1-1.fc38.x86_64.rpm      9.7 MB/s | 313 kB     00:00    
(135/151): libgcc-13.1.1-2.fc38.x86_64.rpm      5.8 MB/s | 106 kB     00:00    
(136/151): libssh-0.10.5-1.fc38.x86_64.rpm       11 MB/s | 211 kB     00:00    
(137/151): libssh-config-0.10.5-1.fc38.noarch.r 440 kB/s | 9.0 kB     00:00    
(138/151): libstdc++-13.1.1-2.fc38.x86_64.rpm    33 MB/s | 860 kB     00:00    
(139/151): libtirpc-1.3.3-1.rc1.fc38.x86_64.rpm 5.4 MB/s |  93 kB     00:00    
(140/151): libgomp-13.1.1-2.fc38.x86_64.rpm     4.5 MB/s | 316 kB     00:00    
(141/151): libxml2-2.10.4-1.fc38.x86_64.rpm      27 MB/s | 701 kB     00:00    
(142/151): libzstd-1.5.5-1.fc38.x86_64.rpm       14 MB/s | 308 kB     00:00    
(143/151): pyproject-srpm-macros-1.7.0-1.fc38.n 817 kB/s |  14 kB     00:00    
(144/151): qt5-srpm-macros-5.15.9-1.fc38.noarch 504 kB/s | 8.1 kB     00:00    
(145/151): rpm-4.18.1-3.fc38.x86_64.rpm          23 MB/s | 570 kB     00:00    
(146/151): rpm-build-libs-4.18.1-3.fc38.x86_64. 5.3 MB/s |  94 kB     00:00    
(147/151): rpm-build-4.18.1-3.fc38.x86_64.rpm   2.8 MB/s |  77 kB     00:00    
(148/151): rpm-libs-4.18.1-3.fc38.x86_64.rpm     15 MB/s | 313 kB     00:00    
(149/151): rpm-sequoia-1.4.0-2.fc38.x86_64.rpm   29 MB/s | 850 kB     00:00    
(150/151): zstd-1.5.5-1.fc38.x86_64.rpm          17 MB/s | 482 kB     00:00    
(151/151): systemd-libs-253.4-1.fc38.x86_64.rpm 5.6 MB/s | 652 kB     00:00    
--------------------------------------------------------------------------------
Total                                            11 MB/s |  53 MB     00:04     
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-3.18-3.fc38.x86_64                          1/1 
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  Installing       : fedora-gpg-keys-38-1.noarch                         22/151 
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  Installing       : setup-2.14.3-2.fc38.noarch                          26/151 
warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.14.3-2.fc38.noarch                          26/151 
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  Installing       : glibc-gconv-extra-2.37-4.fc38.x86_64                32/151 
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  Installing       : glibc-minimal-langpack-2.37-4.fc38.x86_64           33/151 
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  Installing       : libuuid-2.38.1-4.fc38.x86_64                        40/151 
  Installing       : popt-1.19-2.fc38.x86_64                             41/151 
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  Installing       : gmp-1:6.2.1-4.fc38.x86_64                           44/151 
  Installing       : libattr-2.5.1-6.fc38.x86_64                         45/151 
  Installing       : libacl-2.3.1-6.fc38.x86_64                          46/151 
  Installing       : libcap-2.48-6.fc38.x86_64                           47/151 
  Installing       : libxcrypt-4.4.33-7.fc38.x86_64                      48/151 
  Installing       : readline-8.2-3.fc38.x86_64                          49/151 
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  Installing       : dwz-0.15-2.fc38.x86_64                              54/151 
  Installing       : unzip-6.0-60.fc38.x86_64                            55/151 
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  Installing       : libcap-ng-0.8.3-5.fc38.x86_64                       59/151 
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  Installing       : libcom_err-1.46.5-4.fc38.x86_64                     62/151 
  Installing       : libsepol-3.5-1.fc38.x86_64                          63/151 
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  Installing       : libunistring1.0-1.0-1.fc38.x86_64                   65/151 
  Installing       : libidn2-2.3.4-2.fc38.x86_64                         66/151 
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  Installing       : sed-4.8-12.fc38.x86_64                              70/151 
  Installing       : grep-3.8-3.fc38.x86_64                              71/151 
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  Verifying        : cyrus-sasl-lib-2.1.28-9.fc38.x86_64                 14/151 
  Verifying        : debugedit-5.0-7.fc38.x86_64                         15/151 
  Verifying        : diffutils-3.9-1.fc38.x86_64                         16/151 
  Verifying        : dwz-0.15-2.fc38.x86_64                              17/151 
  Verifying        : ed-1.19-2.fc38.x86_64                               18/151 
  Verifying        : efi-srpm-macros-5-7.fc38.noarch                     19/151 
  Verifying        : fedora-gpg-keys-38-1.noarch                         20/151 
  Verifying        : fedora-repos-38-1.noarch                            21/151 
  Verifying        : file-5.44-3.fc38.x86_64                             22/151 
  Verifying        : file-libs-5.44-3.fc38.x86_64                        23/151 
  Verifying        : filesystem-3.18-3.fc38.x86_64                       24/151 
  Verifying        : findutils-1:4.9.0-3.fc38.x86_64                     25/151 
  Verifying        : fonts-srpm-macros-1:2.0.5-11.fc38.noarch            26/151 
  Verifying        : fpc-srpm-macros-1.3-7.fc38.noarch                   27/151 
  Verifying        : gawk-5.1.1-5.fc38.x86_64                            28/151 
  Verifying        : gdbm-libs-1:1.23-3.fc38.x86_64                      29/151 
  Verifying        : ghc-srpm-macros-1.6.1-1.fc38.noarch                 30/151 
  Verifying        : gmp-1:6.2.1-4.fc38.x86_64                           31/151 
  Verifying        : gnat-srpm-macros-6-2.fc38.noarch                    32/151 
  Verifying        : go-srpm-macros-3.2.0-2.fc38.noarch                  33/151 
  Verifying        : grep-3.8-3.fc38.x86_64                              34/151 
  Verifying        : gzip-1.12-3.fc38.x86_64                             35/151 
  Verifying        : info-7.0.2-2.fc38.x86_64                            36/151 
  Verifying        : jansson-2.13.1-6.fc38.x86_64                        37/151 
  Verifying        : kernel-srpm-macros-1.0-16.fc38.noarch               38/151 
  Verifying        : keyutils-libs-1.6.1-6.fc38.x86_64                   39/151 
  Verifying        : krb5-libs-1.20.1-8.fc38.x86_64                      40/151 
  Verifying        : libacl-2.3.1-6.fc38.x86_64                          41/151 
  Verifying        : libarchive-3.6.1-4.fc38.x86_64                      42/151 
  Verifying        : libattr-2.5.1-6.fc38.x86_64                         43/151 
  Verifying        : libblkid-2.38.1-4.fc38.x86_64                       44/151 
  Verifying        : libbrotli-1.0.9-11.fc38.x86_64                      45/151 
  Verifying        : libcap-2.48-6.fc38.x86_64                           46/151 
  Verifying        : libcap-ng-0.8.3-5.fc38.x86_64                       47/151 
  Verifying        : libcom_err-1.46.5-4.fc38.x86_64                     48/151 
  Verifying        : libdb-5.3.28-55.fc38.x86_64                         49/151 
  Verifying        : libeconf-0.4.0-5.fc38.x86_64                        50/151 
  Verifying        : libevent-2.1.12-8.fc38.x86_64                       51/151 
  Verifying        : libfdisk-2.38.1-4.fc38.x86_64                       52/151 
  Verifying        : libffi-3.4.4-2.fc38.x86_64                          53/151 
  Verifying        : libidn2-2.3.4-2.fc38.x86_64                         54/151 
  Verifying        : libmount-2.38.1-4.fc38.x86_64                       55/151 
  Verifying        : libnghttp2-1.52.0-1.fc38.x86_64                     56/151 
  Verifying        : libnsl2-2.0.0-5.fc38.x86_64                         57/151 
  Verifying        : libpkgconf-1.8.0-6.fc38.x86_64                      58/151 
  Verifying        : libpsl-0.21.2-2.fc38.x86_64                         59/151 
  Verifying        : libpwquality-1.4.5-3.fc38.x86_64                    60/151 
  Verifying        : libselinux-3.5-1.fc38.x86_64                        61/151 
  Verifying        : libsemanage-3.5-2.fc38.x86_64                       62/151 
  Verifying        : libsepol-3.5-1.fc38.x86_64                          63/151 
  Verifying        : libsigsegv-2.14-4.fc38.x86_64                       64/151 
  Verifying        : libsmartcols-2.38.1-4.fc38.x86_64                   65/151 
  Verifying        : libtasn1-4.19.0-2.fc38.x86_64                       66/151 
  Verifying        : libunistring1.0-1.0-1.fc38.x86_64                   67/151 
  Verifying        : libutempter-1.2.1-8.fc38.x86_64                     68/151 
  Verifying        : libuuid-2.38.1-4.fc38.x86_64                        69/151 
  Verifying        : libverto-0.3.2-5.fc38.x86_64                        70/151 
  Verifying        : libxcrypt-4.4.33-7.fc38.x86_64                      71/151 
  Verifying        : lua-libs-5.4.4-9.fc38.x86_64                        72/151 
  Verifying        : lua-srpm-macros-1-8.fc38.noarch                     73/151 
  Verifying        : lz4-libs-1.9.4-2.fc38.x86_64                        74/151 
  Verifying        : mpfr-4.1.1-3.fc38.x86_64                            75/151 
  Verifying        : ncurses-base-6.4-3.20230114.fc38.noarch             76/151 
  Verifying        : ncurses-libs-6.4-3.20230114.fc38.x86_64             77/151 
  Verifying        : ocaml-srpm-macros-7-3.fc38.noarch                   78/151 
  Verifying        : openblas-srpm-macros-2-13.fc38.noarch               79/151 
  Verifying        : openldap-2.6.4-1.fc38.x86_64                        80/151 
  Verifying        : openssl-libs-1:3.0.8-2.fc38.x86_64                  81/151 
  Verifying        : p11-kit-0.24.1-6.fc38.x86_64                        82/151 
  Verifying        : p11-kit-trust-0.24.1-6.fc38.x86_64                  83/151 
  Verifying        : package-notes-srpm-macros-0.5-7.fc38.noarch         84/151 
  Verifying        : pam-1.5.2-16.fc38.x86_64                            85/151 
  Verifying        : pam-libs-1.5.2-16.fc38.x86_64                       86/151 
  Verifying        : patch-2.7.6-19.fc38.x86_64                          87/151 
  Verifying        : pcre2-10.42-1.fc38.1.x86_64                         88/151 
  Verifying        : pcre2-syntax-10.42-1.fc38.1.noarch                  89/151 
  Verifying        : perl-srpm-macros-1-48.fc38.noarch                   90/151 
  Verifying        : pkgconf-1.8.0-6.fc38.x86_64                         91/151 
  Verifying        : pkgconf-m4-1.8.0-6.fc38.noarch                      92/151 
  Verifying        : pkgconf-pkg-config-1.8.0-6.fc38.x86_64              93/151 
  Verifying        : popt-1.19-2.fc38.x86_64                             94/151 
  Verifying        : publicsuffix-list-dafsa-20230318-1.fc38.noarch      95/151 
  Verifying        : python-srpm-macros-3.11-10.fc38.noarch              96/151 
  Verifying        : readline-8.2-3.fc38.x86_64                          97/151 
  Verifying        : redhat-rpm-config-252-1.fc38.noarch                 98/151 
  Verifying        : rpmautospec-rpm-macros-0.3.5-1.fc38.noarch          99/151 
  Verifying        : rust-srpm-macros-24-1.fc38.noarch                  100/151 
  Verifying        : sed-4.8-12.fc38.x86_64                             101/151 
  Verifying        : setup-2.14.3-2.fc38.noarch                         102/151 
  Verifying        : shadow-utils-2:4.13-6.fc38.x86_64                  103/151 
  Verifying        : sqlite-libs-3.40.1-2.fc38.x86_64                   104/151 
  Verifying        : tar-2:1.34-8.fc38.x86_64                           105/151 
  Verifying        : tzdata-2023c-1.fc38.noarch                         106/151 
  Verifying        : unzip-6.0-60.fc38.x86_64                           107/151 
  Verifying        : util-linux-2.38.1-4.fc38.x86_64                    108/151 
  Verifying        : util-linux-core-2.38.1-4.fc38.x86_64               109/151 
  Verifying        : which-2.21-39.fc38.x86_64                          110/151 
  Verifying        : xxhash-libs-0.8.1-4.fc38.x86_64                    111/151 
  Verifying        : xz-5.4.1-1.fc38.x86_64                             112/151 
  Verifying        : xz-libs-5.4.1-1.fc38.x86_64                        113/151 
  Verifying        : zip-3.0-36.fc38.x86_64                             114/151 
  Verifying        : zlib-1.2.13-3.fc38.x86_64                          115/151 
  Verifying        : alternatives-1.24-1.fc38.x86_64                    116/151 
  Verifying        : audit-libs-3.1.1-1.fc38.x86_64                     117/151 
  Verifying        : coreutils-9.1-12.fc38.x86_64                       118/151 
  Verifying        : coreutils-common-9.1-12.fc38.x86_64                119/151 
  Verifying        : curl-8.0.1-1.fc38.x86_64                           120/151 
  Verifying        : elfutils-0.189-2.fc38.x86_64                       121/151 
  Verifying        : elfutils-debuginfod-client-0.189-2.fc38.x86_64     122/151 
  Verifying        : elfutils-default-yama-scope-0.189-2.fc38.noarch    123/151 
  Verifying        : elfutils-libelf-0.189-2.fc38.x86_64                124/151 
  Verifying        : elfutils-libs-0.189-2.fc38.x86_64                  125/151 
  Verifying        : fedora-release-38-35.noarch                        126/151 
  Verifying        : fedora-release-common-38-35.noarch                 127/151 
  Verifying        : fedora-release-identity-basic-38-35.noarch         128/151 
  Verifying        : gdb-minimal-13.1-4.fc38.x86_64                     129/151 
  Verifying        : glibc-2.37-4.fc38.x86_64                           130/151 
  Verifying        : glibc-common-2.37-4.fc38.x86_64                    131/151 
  Verifying        : glibc-gconv-extra-2.37-4.fc38.x86_64               132/151 
  Verifying        : glibc-minimal-langpack-2.37-4.fc38.x86_64          133/151 
  Verifying        : libcurl-8.0.1-1.fc38.x86_64                        134/151 
  Verifying        : libgcc-13.1.1-2.fc38.x86_64                        135/151 
  Verifying        : libgomp-13.1.1-2.fc38.x86_64                       136/151 
  Verifying        : libssh-0.10.5-1.fc38.x86_64                        137/151 
  Verifying        : libssh-config-0.10.5-1.fc38.noarch                 138/151 
  Verifying        : libstdc++-13.1.1-2.fc38.x86_64                     139/151 
  Verifying        : libtirpc-1.3.3-1.rc1.fc38.x86_64                   140/151 
  Verifying        : libxml2-2.10.4-1.fc38.x86_64                       141/151 
  Verifying        : libzstd-1.5.5-1.fc38.x86_64                        142/151 
  Verifying        : pyproject-srpm-macros-1.7.0-1.fc38.noarch          143/151 
  Verifying        : qt5-srpm-macros-5.15.9-1.fc38.noarch               144/151 
  Verifying        : rpm-4.18.1-3.fc38.x86_64                           145/151 
  Verifying        : rpm-build-4.18.1-3.fc38.x86_64                     146/151 
  Verifying        : rpm-build-libs-4.18.1-3.fc38.x86_64                147/151 
  Verifying        : rpm-libs-4.18.1-3.fc38.x86_64                      148/151 
  Verifying        : rpm-sequoia-1.4.0-2.fc38.x86_64                    149/151 
  Verifying        : systemd-libs-253.4-1.fc38.x86_64                   150/151 
  Verifying        : zstd-1.5.5-1.fc38.x86_64                           151/151 

Installed:
  alternatives-1.24-1.fc38.x86_64                                               
  ansible-srpm-macros-1-9.1.fc38.noarch                                         
  audit-libs-3.1.1-1.fc38.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-2.39-9.fc38.x86_64                                                   
  binutils-gold-2.39-9.fc38.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-9.1-12.fc38.x86_64                                                  
  coreutils-common-9.1-12.fc38.x86_64                                           
  cpio-2.13-14.fc38.x86_64                                                      
  cracklib-2.9.7-31.fc38.x86_64                                                 
  crypto-policies-20230301-1.gita12f7b2.fc38.noarch                             
  curl-8.0.1-1.fc38.x86_64                                                      
  cyrus-sasl-lib-2.1.28-9.fc38.x86_64                                           
  debugedit-5.0-7.fc38.x86_64                                                   
  diffutils-3.9-1.fc38.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.fc38.x86_64                                                  
  elfutils-debuginfod-client-0.189-2.fc38.x86_64                                
  elfutils-default-yama-scope-0.189-2.fc38.noarch                               
  elfutils-libelf-0.189-2.fc38.x86_64                                           
  elfutils-libs-0.189-2.fc38.x86_64                                             
  fedora-gpg-keys-38-1.noarch                                                   
  fedora-release-38-35.noarch                                                   
  fedora-release-common-38-35.noarch                                            
  fedora-release-identity-basic-38-35.noarch                                    
  fedora-repos-38-1.noarch                                                      
  file-5.44-3.fc38.x86_64                                                       
  file-libs-5.44-3.fc38.x86_64                                                  
  filesystem-3.18-3.fc38.x86_64                                                 
  findutils-1:4.9.0-3.fc38.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-13.1-4.fc38.x86_64                                                
  gdbm-libs-1:1.23-3.fc38.x86_64                                                
  ghc-srpm-macros-1.6.1-1.fc38.noarch                                           
  glibc-2.37-4.fc38.x86_64                                                      
  glibc-common-2.37-4.fc38.x86_64                                               
  glibc-gconv-extra-2.37-4.fc38.x86_64                                          
  glibc-minimal-langpack-2.37-4.fc38.x86_64                                     
  gmp-1:6.2.1-4.fc38.x86_64                                                     
  gnat-srpm-macros-6-2.fc38.noarch                                              
  go-srpm-macros-3.2.0-2.fc38.noarch                                            
  grep-3.8-3.fc38.x86_64                                                        
  gzip-1.12-3.fc38.x86_64                                                       
  info-7.0.2-2.fc38.x86_64                                                      
  jansson-2.13.1-6.fc38.x86_64                                                  
  kernel-srpm-macros-1.0-16.fc38.noarch                                         
  keyutils-libs-1.6.1-6.fc38.x86_64                                             
  krb5-libs-1.20.1-8.fc38.x86_64                                                
  libacl-2.3.1-6.fc38.x86_64                                                    
  libarchive-3.6.1-4.fc38.x86_64                                                
  libattr-2.5.1-6.fc38.x86_64                                                   
  libblkid-2.38.1-4.fc38.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-8.0.1-1.fc38.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-2.38.1-4.fc38.x86_64                                                 
  libffi-3.4.4-2.fc38.x86_64                                                    
  libgcc-13.1.1-2.fc38.x86_64                                                   
  libgomp-13.1.1-2.fc38.x86_64                                                  
  libidn2-2.3.4-2.fc38.x86_64                                                   
  libmount-2.38.1-4.fc38.x86_64                                                 
  libnghttp2-1.52.0-1.fc38.x86_64                                               
  libnsl2-2.0.0-5.fc38.x86_64                                                   
  libpkgconf-1.8.0-6.fc38.x86_64                                                
  libpsl-0.21.2-2.fc38.x86_64                                                   
  libpwquality-1.4.5-3.fc38.x86_64                                              
  libselinux-3.5-1.fc38.x86_64                                                  
  libsemanage-3.5-2.fc38.x86_64                                                 
  libsepol-3.5-1.fc38.x86_64                                                    
  libsigsegv-2.14-4.fc38.x86_64                                                 
  libsmartcols-2.38.1-4.fc38.x86_64                                             
  libssh-0.10.5-1.fc38.x86_64                                                   
  libssh-config-0.10.5-1.fc38.noarch                                            
  libstdc++-13.1.1-2.fc38.x86_64                                                
  libtasn1-4.19.0-2.fc38.x86_64                                                 
  libtirpc-1.3.3-1.rc1.fc38.x86_64                                              
  libunistring1.0-1.0-1.fc38.x86_64                                             
  libutempter-1.2.1-8.fc38.x86_64                                               
  libuuid-2.38.1-4.fc38.x86_64                                                  
  libverto-0.3.2-5.fc38.x86_64                                                  
  libxcrypt-4.4.33-7.fc38.x86_64                                                
  libxml2-2.10.4-1.fc38.x86_64                                                  
  libzstd-1.5.5-1.fc38.x86_64                                                   
  lua-libs-5.4.4-9.fc38.x86_64                                                  
  lua-srpm-macros-1-8.fc38.noarch                                               
  lz4-libs-1.9.4-2.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                                       
  ocaml-srpm-macros-7-3.fc38.noarch                                             
  openblas-srpm-macros-2-13.fc38.noarch                                         
  openldap-2.6.4-1.fc38.x86_64                                                  
  openssl-libs-1:3.0.8-2.fc38.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-1.5.2-16.fc38.x86_64                                                      
  pam-libs-1.5.2-16.fc38.x86_64                                                 
  patch-2.7.6-19.fc38.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-1.8.0-6.fc38.x86_64                                                   
  pkgconf-m4-1.8.0-6.fc38.noarch                                                
  pkgconf-pkg-config-1.8.0-6.fc38.x86_64                                        
  popt-1.19-2.fc38.x86_64                                                       
  publicsuffix-list-dafsa-20230318-1.fc38.noarch                                
  pyproject-srpm-macros-1.7.0-1.fc38.noarch                                     
  python-srpm-macros-3.11-10.fc38.noarch                                        
  qt5-srpm-macros-5.15.9-1.fc38.noarch                                          
  readline-8.2-3.fc38.x86_64                                                    
  redhat-rpm-config-252-1.fc38.noarch                                           
  rpm-4.18.1-3.fc38.x86_64                                                      
  rpm-build-4.18.1-3.fc38.x86_64                                                
  rpm-build-libs-4.18.1-3.fc38.x86_64                                           
  rpm-libs-4.18.1-3.fc38.x86_64                                                 
  rpm-sequoia-1.4.0-2.fc38.x86_64                                               
  rpmautospec-rpm-macros-0.3.5-1.fc38.noarch                                    
  rust-srpm-macros-24-1.fc38.noarch                                             
  sed-4.8-12.fc38.x86_64                                                        
  setup-2.14.3-2.fc38.noarch                                                    
  shadow-utils-2:4.13-6.fc38.x86_64                                             
  sqlite-libs-3.40.1-2.fc38.x86_64                                              
  systemd-libs-253.4-1.fc38.x86_64                                              
  tar-2:1.34-8.fc38.x86_64                                                      
  tzdata-2023c-1.fc38.noarch                                                    
  unzip-6.0-60.fc38.x86_64                                                      
  util-linux-2.38.1-4.fc38.x86_64                                               
  util-linux-core-2.38.1-4.fc38.x86_64                                          
  which-2.21-39.fc38.x86_64                                                     
  xxhash-libs-0.8.1-4.fc38.x86_64                                               
  xz-5.4.1-1.fc38.x86_64                                                        
  xz-libs-5.4.1-1.fc38.x86_64                                                   
  zip-3.0-36.fc38.x86_64                                                        
  zlib-1.2.13-3.fc38.x86_64                                                     
  zstd-1.5.5-1.fc38.x86_64                                                      

Complete!
Finish: dnf install
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: keyutils-libs-1.6.1-6.fc38.x86_64
lua-libs-5.4.4-9.fc38.x86_64
tar-1.34-8.fc38.x86_64
filesystem-3.18-3.fc38.x86_64
pcre2-10.42-1.fc38.1.x86_64
pkgconf-pkg-config-1.8.0-6.fc38.x86_64
libgcc-13.1.1-2.fc38.x86_64
pam-libs-1.5.2-16.fc38.x86_64
pkgconf-m4-1.8.0-6.fc38.noarch
bash-5.2.15-3.fc38.x86_64
libutempter-1.2.1-8.fc38.x86_64
efi-srpm-macros-5-7.fc38.noarch
jansson-2.13.1-6.fc38.x86_64
dwz-0.15-2.fc38.x86_64
libbrotli-1.0.9-11.fc38.x86_64
libpsl-0.21.2-2.fc38.x86_64
tzdata-2023c-1.fc38.noarch
sed-4.8-12.fc38.x86_64
ocaml-srpm-macros-7-3.fc38.noarch
curl-8.0.1-1.fc38.x86_64
openssl-libs-3.0.8-2.fc38.x86_64
gnat-srpm-macros-6-2.fc38.noarch
ncurses-base-6.4-3.20230114.fc38.noarch
libevent-2.1.12-8.fc38.x86_64
perl-srpm-macros-1-48.fc38.noarch
libgomp-13.1.1-2.fc38.x86_64
rpm-build-libs-4.18.1-3.fc38.x86_64
lua-srpm-macros-1-8.fc38.noarch
libstdc++-13.1.1-2.fc38.x86_64
libpkgconf-1.8.0-6.fc38.x86_64
file-libs-5.44-3.fc38.x86_64
fedora-release-common-38-35.noarch
fedora-repos-38-1.noarch
ed-1.19-2.fc38.x86_64
info-7.0.2-2.fc38.x86_64
libacl-2.3.1-6.fc38.x86_64
kernel-srpm-macros-1.0-16.fc38.noarch
zlib-1.2.13-3.fc38.x86_64
ncurses-libs-6.4-3.20230114.fc38.x86_64
binutils-gold-2.39-9.fc38.x86_64
authselect-1.4.2-2.fc38.x86_64
cracklib-2.9.7-31.fc38.x86_64
libssh-config-0.10.5-1.fc38.noarch
cpio-2.13-14.fc38.x86_64
binutils-2.39-9.fc38.x86_64
libmount-2.38.1-4.fc38.x86_64
authselect-libs-1.4.2-2.fc38.x86_64
rpm-4.18.1-3.fc38.x86_64
gdb-minimal-13.1-4.fc38.x86_64
xz-5.4.1-1.fc38.x86_64
libssh-0.10.5-1.fc38.x86_64
libzstd-1.5.5-1.fc38.x86_64
audit-libs-3.1.1-1.fc38.x86_64
popt-1.19-2.fc38.x86_64
rpm-sequoia-1.4.0-2.fc38.x86_64
zip-3.0-36.fc38.x86_64
libsepol-3.5-1.fc38.x86_64
pam-1.5.2-16.fc38.x86_64
rpm-libs-4.18.1-3.fc38.x86_64
bzip2-1.0.8-13.fc38.x86_64
elfutils-libelf-0.189-2.fc38.x86_64
libsemanage-3.5-2.fc38.x86_64
gmp-6.2.1-4.fc38.x86_64
file-5.44-3.fc38.x86_64
openldap-2.6.4-1.fc38.x86_64
libsigsegv-2.14-4.fc38.x86_64
fonts-srpm-macros-2.0.5-11.fc38.noarch
glibc-minimal-langpack-2.37-4.fc38.x86_64
util-linux-2.38.1-4.fc38.x86_64
sqlite-libs-3.40.1-2.fc38.x86_64
xz-libs-5.4.1-1.fc38.x86_64
fedora-release-38-35.noarch
util-linux-core-2.38.1-4.fc38.x86_64
diffutils-3.9-1.fc38.x86_64
p11-kit-trust-0.24.1-6.fc38.x86_64
libnghttp2-1.52.0-1.fc38.x86_64
rpm-build-4.18.1-3.fc38.x86_64
libverto-0.3.2-5.fc38.x86_64
libffi-3.4.4-2.fc38.x86_64
ansible-srpm-macros-1-9.1.fc38.noarch
libxcrypt-4.4.33-7.fc38.x86_64
gzip-1.12-3.fc38.x86_64
elfutils-libs-0.189-2.fc38.x86_64
libblkid-2.38.1-4.fc38.x86_64
libattr-2.5.1-6.fc38.x86_64
ca-certificates-2023.2.60-2.fc38.noarch
gdbm-libs-1.23-3.fc38.x86_64
findutils-4.9.0-3.fc38.x86_64
libxml2-2.10.4-1.fc38.x86_64
libnsl2-2.0.0-5.fc38.x86_64
libpwquality-1.4.5-3.fc38.x86_64
libcurl-8.0.1-1.fc38.x86_64
lz4-libs-1.9.4-2.fc38.x86_64
libcap-ng-0.8.3-5.fc38.x86_64
rpmautospec-rpm-macros-0.3.5-1.fc38.noarch
openblas-srpm-macros-2-13.fc38.noarch
systemd-libs-253.4-1.fc38.x86_64
xxhash-libs-0.8.1-4.fc38.x86_64
libtasn1-4.19.0-2.fc38.x86_64
basesystem-11-15.fc38.noarch
shadow-utils-4.13-6.fc38.x86_64
elfutils-0.189-2.fc38.x86_64
cyrus-sasl-lib-2.1.28-9.fc38.x86_64
fedora-gpg-keys-38-1.noarch
libidn2-2.3.4-2.fc38.x86_64
glibc-gconv-extra-2.37-4.fc38.x86_64
libuuid-2.38.1-4.fc38.x86_64
p11-kit-0.24.1-6.fc38.x86_64
libsmartcols-2.38.1-4.fc38.x86_64
redhat-rpm-config-252-1.fc38.noarch
crypto-policies-20230301-1.gita12f7b2.fc38.noarch
coreutils-9.1-12.fc38.x86_64
patch-2.7.6-19.fc38.x86_64
pcre2-syntax-10.42-1.fc38.1.noarch
readline-8.2-3.fc38.x86_64
libtirpc-1.3.3-1.rc1.fc38.x86_64
glibc-2.37-4.fc38.x86_64
coreutils-common-9.1-12.fc38.x86_64
alternatives-1.24-1.fc38.x86_64
krb5-libs-1.20.1-8.fc38.x86_64
fedora-release-identity-basic-38-35.noarch
fpc-srpm-macros-1.3-7.fc38.noarch
grep-3.8-3.fc38.x86_64
publicsuffix-list-dafsa-20230318-1.fc38.noarch
gpg-pubkey-eb10b464-6202d9c6
setup-2.14.3-2.fc38.noarch
libeconf-0.4.0-5.fc38.x86_64
which-2.21-39.fc38.x86_64
libunistring1.0-1.0-1.fc38.x86_64
libdb-5.3.28-55.fc38.x86_64
libselinux-3.5-1.fc38.x86_64
pyproject-srpm-macros-1.7.0-1.fc38.noarch
libfdisk-2.38.1-4.fc38.x86_64
libarchive-3.6.1-4.fc38.x86_64
libcap-2.48-6.fc38.x86_64
bzip2-libs-1.0.8-13.fc38.x86_64
unzip-6.0-60.fc38.x86_64
gawk-5.1.1-5.fc38.x86_64
go-srpm-macros-3.2.0-2.fc38.noarch
qt5-srpm-macros-5.15.9-1.fc38.noarch
elfutils-debuginfod-client-0.189-2.fc38.x86_64
python-srpm-macros-3.11-10.fc38.noarch
elfutils-default-yama-scope-0.189-2.fc38.noarch
zstd-1.5.5-1.fc38.x86_64
libcom_err-1.46.5-4.fc38.x86_64
debugedit-5.0-7.fc38.x86_64
rust-srpm-macros-24-1.fc38.noarch
mpfr-4.1.1-3.fc38.x86_64
pkgconf-1.8.0-6.fc38.x86_64
ghc-srpm-macros-1.6.1-1.fc38.noarch
glibc-common-2.37-4.fc38.x86_64
package-notes-srpm-macros-0.5-7.fc38.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-7.520-1.20230516221152439026.pr1.fc38.src.rpm
Finish: rpmbuild -bs
cp: ‘var/lib/mock/fedora-38-x86_64-1684275155.629876/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-38-x86_64-1684275155.629876/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-38-x86_64-1684275155.629876/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-38-x86_64-1684275155.629876/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-4nnaj2wf/mafft/mafft.spec) Config(child) 2 minutes 4 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-7.520-1.20230516221152439026.pr1.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1684275155.629876 -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-7.520-1.20230516221152439026.pr1.fc38.src.rpm)  Config(fedora-38-x86_64)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-38-x86_64-bootstrap-1684275155.629876/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-38-x86_64-bootstrap-1684275155.629876/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-38-x86_64-1684275155.629876/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                                  30 kB/s | 1.5 kB     00:00    
fedora                                          577 kB/s |  26 kB     00:00    
updates                                         568 kB/s |  23 kB     00:00    
Dependencies resolved.
Nothing to do.
Complete!
Finish: dnf update
Finish: chroot init
Start: build phase for mafft-7.520-1.20230516221152439026.pr1.fc38.src.rpm
Start: build setup for mafft-7.520-1.20230516221152439026.pr1.fc38.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-7.520-1.20230516221152439026.pr1.fc38.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  32 kB/s | 1.5 kB     00:00    
fedora                                          523 kB/s |  26 kB     00:00    
updates                                         543 kB/s |  23 kB     00:00    
Dependencies resolved.
================================================================================
 Package                  Architecture Version              Repository     Size
================================================================================
Installing:
 gcc                      x86_64       13.1.1-2.fc38        updates        34 M
 gcc-c++                  x86_64       13.1.1-2.fc38        updates        13 M
 make                     x86_64       1:4.4-3.fc38         fedora        580 k
 zlib-devel               x86_64       1.2.13-3.fc38        fedora         45 k
Installing dependencies:
 annobin-docs             noarch       12.10-1.fc38         updates        94 k
 annobin-plugin-gcc       x86_64       12.10-1.fc38         updates       893 k
 cpp                      x86_64       13.1.1-2.fc38        updates        11 M
 gc                       x86_64       8.2.2-3.fc38         fedora        110 k
 gcc-plugin-annobin       x86_64       13.1.1-2.fc38        updates        43 k
 glibc-devel              x86_64       2.37-4.fc38          updates        52 k
 glibc-headers-x86        noarch       2.37-4.fc38          updates       532 k
 guile22                  x86_64       2.2.7-7.fc38         fedora        6.5 M
 kernel-headers           x86_64       6.2.6-300.fc38       fedora        1.5 M
 libmpc                   x86_64       1.3.1-2.fc38         fedora         70 k
 libstdc++-devel          x86_64       13.1.1-2.fc38        updates       2.6 M
 libtool-ltdl             x86_64       2.4.7-6.fc38         fedora         37 k
 libxcrypt-devel          x86_64       4.4.33-7.fc38        fedora         30 k

Transaction Summary
================================================================================
Install  17 Packages

Total download size: 71 M
Installed size: 227 M
Downloading Packages:
(1/17): gc-8.2.2-3.fc38.x86_64.rpm              285 kB/s | 110 kB     00:00    
(2/17): libmpc-1.3.1-2.fc38.x86_64.rpm          668 kB/s |  70 kB     00:00    
(3/17): libtool-ltdl-2.4.7-6.fc38.x86_64.rpm    402 kB/s |  37 kB     00:00    
(4/17): libxcrypt-devel-4.4.33-7.fc38.x86_64.rp 351 kB/s |  30 kB     00:00    
(5/17): kernel-headers-6.2.6-300.fc38.x86_64.rp 2.2 MB/s | 1.5 MB     00:00    
(6/17): zlib-devel-1.2.13-3.fc38.x86_64.rpm     603 kB/s |  45 kB     00:00    
(7/17): make-4.4-3.fc38.x86_64.rpm              2.1 MB/s | 580 kB     00:00    
(8/17): guile22-2.2.7-7.fc38.x86_64.rpm         6.9 MB/s | 6.5 MB     00:00    
(9/17): annobin-docs-12.10-1.fc38.noarch.rpm    226 kB/s |  94 kB     00:00    
(10/17): annobin-plugin-gcc-12.10-1.fc38.x86_64 2.6 MB/s | 893 kB     00:00    
(11/17): cpp-13.1.1-2.fc38.x86_64.rpm            13 MB/s |  11 MB     00:00    
(12/17): gcc-plugin-annobin-13.1.1-2.fc38.x86_6 1.1 MB/s |  43 kB     00:00    
(13/17): glibc-devel-2.37-4.fc38.x86_64.rpm     1.3 MB/s |  52 kB     00:00    
(14/17): glibc-headers-x86-2.37-4.fc38.noarch.r  10 MB/s | 532 kB     00:00    
(15/17): libstdc++-devel-13.1.1-2.fc38.x86_64.r  21 MB/s | 2.6 MB     00:00    
(16/17): gcc-13.1.1-2.fc38.x86_64.rpm            38 MB/s |  34 MB     00:00    
(17/17): gcc-c++-13.1.1-2.fc38.x86_64.rpm        14 MB/s |  13 MB     00:00    
--------------------------------------------------------------------------------
Total                                            30 MB/s |  71 MB     00:02     
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                            1/17 
  Installing       : cpp-13.1.1-2.fc38.x86_64                              2/17 
  Installing       : libstdc++-devel-13.1.1-2.fc38.x86_64                  3/17 
  Installing       : glibc-headers-x86-2.37-4.fc38.noarch                  4/17 
  Installing       : annobin-docs-12.10-1.fc38.noarch                      5/17 
  Installing       : libtool-ltdl-2.4.7-6.fc38.x86_64                      6/17 
  Installing       : kernel-headers-6.2.6-300.fc38.x86_64                  7/17 
  Installing       : libxcrypt-devel-4.4.33-7.fc38.x86_64                  8/17 
  Installing       : glibc-devel-2.37-4.fc38.x86_64                        9/17 
  Installing       : gc-8.2.2-3.fc38.x86_64                               10/17 
  Installing       : guile22-2.2.7-7.fc38.x86_64                          11/17 
  Installing       : make-1:4.4-3.fc38.x86_64                             12/17 
  Installing       : gcc-13.1.1-2.fc38.x86_64                             13/17 
  Running scriptlet: gcc-13.1.1-2.fc38.x86_64                             13/17 
  Installing       : annobin-plugin-gcc-12.10-1.fc38.x86_64               14/17 
  Running scriptlet: annobin-plugin-gcc-12.10-1.fc38.x86_64               14/17 
  Installing       : gcc-c++-13.1.1-2.fc38.x86_64                         15/17 
  Installing       : gcc-plugin-annobin-13.1.1-2.fc38.x86_64              16/17 
  Running scriptlet: gcc-plugin-annobin-13.1.1-2.fc38.x86_64              16/17 
  Installing       : zlib-devel-1.2.13-3.fc38.x86_64                      17/17 
  Running scriptlet: zlib-devel-1.2.13-3.fc38.x86_64                      17/17 
  Verifying        : gc-8.2.2-3.fc38.x86_64                                1/17 
  Verifying        : guile22-2.2.7-7.fc38.x86_64                           2/17 
  Verifying        : kernel-headers-6.2.6-300.fc38.x86_64                  3/17 
  Verifying        : libmpc-1.3.1-2.fc38.x86_64                            4/17 
  Verifying        : libtool-ltdl-2.4.7-6.fc38.x86_64                      5/17 
  Verifying        : libxcrypt-devel-4.4.33-7.fc38.x86_64                  6/17 
  Verifying        : make-1:4.4-3.fc38.x86_64                              7/17 
  Verifying        : zlib-devel-1.2.13-3.fc38.x86_64                       8/17 
  Verifying        : annobin-docs-12.10-1.fc38.noarch                      9/17 
  Verifying        : annobin-plugin-gcc-12.10-1.fc38.x86_64               10/17 
  Verifying        : cpp-13.1.1-2.fc38.x86_64                             11/17 
  Verifying        : gcc-13.1.1-2.fc38.x86_64                             12/17 
  Verifying        : gcc-c++-13.1.1-2.fc38.x86_64                         13/17 
  Verifying        : gcc-plugin-annobin-13.1.1-2.fc38.x86_64              14/17 
  Verifying        : glibc-devel-2.37-4.fc38.x86_64                       15/17 
  Verifying        : glibc-headers-x86-2.37-4.fc38.noarch                 16/17 
  Verifying        : libstdc++-devel-13.1.1-2.fc38.x86_64                 17/17 

Installed:
  annobin-docs-12.10-1.fc38.noarch                                              
  annobin-plugin-gcc-12.10-1.fc38.x86_64                                        
  cpp-13.1.1-2.fc38.x86_64                                                      
  gc-8.2.2-3.fc38.x86_64                                                        
  gcc-13.1.1-2.fc38.x86_64                                                      
  gcc-c++-13.1.1-2.fc38.x86_64                                                  
  gcc-plugin-annobin-13.1.1-2.fc38.x86_64                                       
  glibc-devel-2.37-4.fc38.x86_64                                                
  glibc-headers-x86-2.37-4.fc38.noarch                                          
  guile22-2.2.7-7.fc38.x86_64                                                   
  kernel-headers-6.2.6-300.fc38.x86_64                                          
  libmpc-1.3.1-2.fc38.x86_64                                                    
  libstdc++-devel-13.1.1-2.fc38.x86_64                                          
  libtool-ltdl-2.4.7-6.fc38.x86_64                                              
  libxcrypt-devel-4.4.33-7.fc38.x86_64                                          
  make-1:4.4-3.fc38.x86_64                                                      
  zlib-devel-1.2.13-3.fc38.x86_64                                               

Complete!
Finish: build setup for mafft-7.520-1.20230516221152439026.pr1.fc38.src.rpm
Start: rpmbuild mafft-7.520-1.20230516221152439026.pr1.fc38.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.W90ilf
+ 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.qu3xHf
+ 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
+ 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:556:14: note: in a call to allocation function 'calloc' declared here
  556 | 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:556:14: note: in a call to allocation function 'calloc' declared here
  556 | 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:906,
                 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:556:14: note: in a call to allocation function 'calloc' declared here
  556 | 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:556:14: note: in a call to allocation function 'calloc' declared here
  556 | 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:906,
                 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:556:14: note: in a call to allocation function 'calloc' declared here
  556 | 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:556:14: note: in a call to allocation function 'calloc' declared here
  556 | 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:906,
                 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.aOnkRB
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.x86_64
++ dirname /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.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
+ 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-7.520-1.20230516221152439026.pr1.fc38.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-7.520-1.20230516221152439026.pr1.fc38.x86_64/usr/local/libexec/mafft
chmod 755 /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.x86_64/usr/local/libexec/mafft
mkdir -p /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.x86_64/usr/local/bin
chmod 755 /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.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-7.520-1.20230516221152439026.pr1.fc38.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-7.520-1.20230516221152439026.pr1.fc38.x86_64/usr/local/libexec/mafft
/usr/bin/install -p mafftash_premafft.pl seekquencer_premafft.pl /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.x86_64/usr/local/libexec/mafft
( cd /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.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-7.520-1.20230516221152439026.pr1.fc38.x86_64/usr/local/share/man/man1
chmod 755 /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.x86_64/usr/local/share/man/man1
/usr/bin/install -p -m 644 mafft.1 mafft-homologs.1 /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.x86_64/usr/local/share/man/man1
+ cd ../extensions
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.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-7.520-1.20230516221152439026.pr1.fc38.x86_64/usr/local/libexec/mafft
chmod 755 /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.x86_64/usr/local/libexec/mafft
chmod 755 mxscarnamod
/usr/bin/install -p mxscarnamod /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.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-7.520-1.20230516221152439026.pr1.fc38.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 = 7.520-1.20230516221152439026.pr1.fc38 mafft(x86-64) = 7.520-1.20230516221152439026.pr1.fc38
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 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_2.4)(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-7.520-1.20230516221152439026.pr1.fc38.x86_64
Wrote: /builddir/build/RPMS/mafft-7.520-1.20230516221152439026.pr1.fc38.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.YZlSVF
+ umask 022
+ cd /builddir/build/BUILD
+ cd mafft-v7.520
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/mafft-7.520-1.20230516221152439026.pr1.fc38.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.m4UdiQ
+ 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-7.520-1.20230516221152439026.pr1.fc38.src.rpm
Finish: build phase for mafft-7.520-1.20230516221152439026.pr1.fc38.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-38-x86_64-1684275155.629876/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-38-x86_64-1684275155.629876/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-38-x86_64-1684275155.629876/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/mafft-7.520-1.20230516221152439026.pr1.fc38.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