Warning: Permanently added '128.168.143.156' (ED25519) to the list of known hosts.
Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5174200 --chroot fedora-rawhide-s390x --detached
Version: 0.62
PID: 13325
Logging PID: 13326
Task:
{'appstream': False,
 'background': True,
 'build_id': 5174200,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-s390x',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '8a2eaf4d26f44c0df2ba49251d3666a8b439c286',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/percolator',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'percolator',
 'package_version': '3.05-10',
 'project_dirname': 'gcc-13-test',
 'project_name': 'gcc-13-test',
 'project_owner': 'jakub',
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jakub/gcc-13-test/fedora-rawhide-s390x/',
            'id': 'copr_base',
            'name': 'Copr repository'},
           {'baseurl': 'https://jakub.fedorapeople.org/fedora-gcc13-$arch/',
            'id': 'https_jakub_fedorapeople_org_fedora_gcc13_arch',
            'name': 'Additional repo https_jakub_fedorapeople_org_fedora_gcc13_arch'}],
 'sandbox': 'jakub/gcc-13-test--jakub',
 'source_json': {},
 'source_type': None,
 'submitter': 'jakub',
 'tags': [],
 'task_id': '5174200-fedora-rawhide-s390x',
 'timeout': 115200,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/percolator /var/lib/copr-rpmbuild/workspace/workdir-jo428f29/percolator --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/percolator', '/var/lib/copr-rpmbuild/workspace/workdir-jo428f29/percolator', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-jo428f29/percolator'...

Running: git checkout 8a2eaf4d26f44c0df2ba49251d3666a8b439c286

cmd: ['git', 'checkout', '8a2eaf4d26f44c0df2ba49251d3666a8b439c286']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-jo428f29/percolator
rc: 0
stdout: 
stderr: Note: switching to '8a2eaf4d26f44c0df2ba49251d3666a8b439c286'.

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 8a2eaf4 automatic import of percolator

Running: copr-distgit-client sources
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-jo428f29/percolator
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 percolator-rel-3-05.tar.gz
INFO: Calling: curl -H Pragma: -o percolator-rel-3-05.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jakub/gcc-13-test/percolator/percolator-rel-3-05.tar.gz/md5/46a10770d808f8db4bd5bd2d30c9be4d/percolator-rel-3-05.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 11.5M  100 11.5M    0     0  5633k      0  0:00:02  0:00:02 --:--:-- 5633k
INFO: Reading stdout from command: md5sum percolator-rel-3-05.tar.gz
INFO: Downloading yeast-01.sqt.tar.gz
INFO: Calling: curl -H Pragma: -o yeast-01.sqt.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jakub/gcc-13-test/percolator/yeast-01.sqt.tar.gz/md5/81e1997e1c1c193cbfcd4eb54c706af9/yeast-01.sqt.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 47.9M  100 47.9M    0     0  11.8M      0  0:00:04  0:00:04 --:--:-- 11.8M
INFO: Reading stdout from command: md5sum yeast-01.sqt.tar.gz

Running (timeout=115200): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-jo428f29/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-jo428f29/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1672058577.895426 -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-jo428f29/percolator/percolator.spec)  Config(fedora-rawhide-s390x)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1672058577.895426/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                                  30 MB/s |  29 MB     00:00    
Additional repo https_jakub_fedorapeople_org_fe  47 kB/s |  86 kB     00:01    
fedora                                           11 MB/s |  59 MB     00:05    
Last metadata expiration check: 0:00:01 ago on Mon Dec 26 12:43:14 2022.
Dependencies resolved.
=========================================================================================================================
 Package                         Arch    Version                    Repository                                       Size
=========================================================================================================================
Installing:
 dnf                             noarch  4.14.0-1.fc38              fedora                                          480 k
 dnf-plugins-core                noarch  4.3.1-1.fc38               fedora                                           34 k
Installing dependencies:
 alternatives                    s390x   1.21-1.fc38                copr_base                                        39 k
 audit-libs                      s390x   3.0.9-2.fc38               fedora                                          114 k
 basesystem                      noarch  11-14.fc37                 fedora                                          7.0 k
 bash                            s390x   5.2.9-3.fc38               copr_base                                       1.8 M
 bzip2-libs                      s390x   1.0.8-12.fc38              copr_base                                        47 k
 ca-certificates                 noarch  2022.2.54-5.fc37           fedora                                          829 k
 coreutils                       s390x   9.1-8.fc38                 copr_base                                       1.1 M
 coreutils-common                s390x   9.1-8.fc38                 copr_base                                       2.0 M
 crypto-policies                 noarch  20221215-1.gita4c31a3.fc38 fedora                                           90 k
 curl                            s390x   7.87.0-1.fc38              copr_base                                       345 k
 cyrus-sasl-lib                  s390x   2.1.28-8.fc38              copr_base                                       773 k
 dbus-libs                       s390x   1:1.14.4-1.fc38            copr_base                                       159 k
 dnf-data                        noarch  4.14.0-1.fc38              fedora                                           43 k
 elfutils-default-yama-scope     noarch  0.188-3.fc38               copr_base                                        16 k
 elfutils-libelf                 s390x   0.188-3.fc38               copr_base                                       202 k
 elfutils-libs                   s390x   0.188-3.fc38               copr_base                                       275 k
 expat                           s390x   2.5.0-1.fc38               copr_base                                       114 k
 fedora-gpg-keys                 noarch  38-0.3                     fedora                                          125 k
 fedora-release                  noarch  38-0.6                     fedora                                           11 k
 fedora-release-common           noarch  38-0.6                     fedora                                           21 k
 fedora-release-identity-basic   noarch  38-0.6                     fedora                                           11 k
 fedora-repos                    noarch  38-0.3                     fedora                                           10 k
 fedora-repos-rawhide            noarch  38-0.3                     fedora                                          9.7 k
 file-libs                       s390x   5.42-4.fc38                copr_base                                       683 k
 filesystem                      s390x   3.18-2.fc37                fedora                                          1.1 M
 findutils                       s390x   1:4.9.0-2.fc38             copr_base                                       489 k
 gawk                            s390x   5.1.1-4.fc38               copr_base                                       1.0 M
 gdbm-libs                       s390x   1:1.23-2.fc38              copr_base                                        59 k
 glib2                           s390x   2.74.1-2.fc38              copr_base                                       2.7 M
 glibc                           s390x   2.36.9000-19.fc38          fedora                                          1.6 M
 glibc-common                    s390x   2.36.9000-19.fc38          fedora                                          306 k
 glibc-minimal-langpack          s390x   2.36.9000-19.fc38          fedora                                           30 k
 gmp                             s390x   1:6.2.1-3.fc38             copr_base                                       326 k
 gnupg2                          s390x   2.3.8-1.fc38               copr_base                                       2.6 M
 gnutls                          s390x   3.7.8-9.fc38               copr_base                                       1.0 M
 gpgme                           s390x   1.17.1-3.fc38              copr_base                                       219 k
 grep                            s390x   3.8-1.fc38                 copr_base                                       290 k
 ima-evm-utils                   s390x   1.4-6.fc38                 copr_base                                        63 k
 json-c                          s390x   0.16-3.fc38                copr_base                                        43 k
 keyutils-libs                   s390x   1.6.1-5.fc38               copr_base                                        32 k
 krb5-libs                       s390x   1.20.1-3.fc38              copr_base                                       735 k
 libacl                          s390x   2.3.1-4.fc38               copr_base                                        25 k
 libarchive                      s390x   3.6.1-3.fc38               copr_base                                       426 k
 libassuan                       s390x   2.5.5-5.fc38               copr_base                                        67 k
 libattr                         s390x   2.5.1-5.fc38               copr_base                                        19 k
 libb2                           s390x   0.98.1-7.fc38              copr_base                                        27 k
 libblkid                        s390x   2.38.1-3.fc38              fedora                                          103 k
 libbrotli                       s390x   1.0.9-9.fc38               copr_base                                       344 k
 libcap                          s390x   2.48-5.fc38                copr_base                                        68 k
 libcap-ng                       s390x   0.8.3-4.fc38               copr_base                                        33 k
 libcom_err                      s390x   1.46.5-3.fc38              copr_base                                        26 k
 libcomps                        s390x   0.1.18-4.fc38              copr_base                                        81 k
 libcurl                         s390x   7.87.0-1.fc38              copr_base                                       320 k
 libdnf                          s390x   0.68.0-1.fc38              copr_base                                       653 k
 libevent                        s390x   2.1.12-7.fc38              copr_base                                       260 k
 libffi                          s390x   3.4.4-1.fc38               copr_base                                        36 k
 libfsverity                     s390x   1.4-8.fc38                 copr_base                                        20 k
 libgcc                          s390x   13.0.0-0.4.fc38            https_jakub_fedorapeople_org_fedora_gcc13_arch   66 k
 libgcrypt                       s390x   1.10.1-6.fc38              copr_base                                       495 k
 libgomp                         s390x   13.0.0-0.4.fc38            https_jakub_fedorapeople_org_fedora_gcc13_arch  305 k
 libgpg-error                    s390x   1.46-1.fc38                copr_base                                       225 k
 libidn2                         s390x   2.3.4-1.fc38               copr_base                                       155 k
 libksba                         s390x   1.6.3-1.fc38               copr_base                                       163 k
 libmodulemd                     s390x   2.14.0-4.fc38              copr_base                                       220 k
 libmount                        s390x   2.38.1-3.fc38              fedora                                          132 k
 libnghttp2                      s390x   1.51.0-1.fc38              copr_base                                        78 k
 libnsl2                         s390x   2.0.0-4.fc38               copr_base                                        30 k
 libpsl                          s390x   0.21.1-6.fc38              copr_base                                        66 k
 librepo                         s390x   1.15.1-1.fc38              copr_base                                        96 k
 libreport-filesystem            noarch  2.17.6-1.fc38              copr_base                                        14 k
 libselinux                      s390x   3.4-6.fc38                 copr_base                                        91 k
 libsemanage                     s390x   3.4-6.fc38                 copr_base                                       122 k
 libsepol                        s390x   3.4-4.fc38                 copr_base                                       330 k
 libsigsegv                      s390x   2.14-3.fc38                copr_base                                        27 k
 libsmartcols                    s390x   2.38.1-3.fc38              fedora                                           63 k
 libsolv                         s390x   0.7.22-3.fc38              copr_base                                       443 k
 libssh                          s390x   0.10.4-2.fc38              copr_base                                       206 k
 libssh-config                   noarch  0.10.4-2.fc38              copr_base                                       9.2 k
 libstdc++                       s390x   13.0.0-0.4.fc38            https_jakub_fedorapeople_org_fedora_gcc13_arch  889 k
 libtasn1                        s390x   4.19.0-1.fc38              copr_base                                        78 k
 libtirpc                        s390x   1.3.3-0.fc38               copr_base                                        97 k
 libunistring                    s390x   1.0-2.fc38                 copr_base                                       552 k
 libuuid                         s390x   2.38.1-3.fc38              fedora                                           27 k
 libverto                        s390x   0.3.2-4.fc38               copr_base                                        21 k
 libxcrypt                       s390x   4.4.33-5.fc38              copr_base                                       125 k
 libxml2                         s390x   2.10.3-2.fc38              copr_base                                       714 k
 libyaml                         s390x   0.2.5-8.fc38               copr_base                                        62 k
 libzstd                         s390x   1.5.2-3.fc37               fedora                                          274 k
 lua-libs                        s390x   5.4.4-6.fc38               copr_base                                       141 k
 lz4-libs                        s390x   1.9.3-5.fc38               copr_base                                        88 k
 mpdecimal                       s390x   2.5.1-4.fc38               copr_base                                       115 k
 mpfr                            s390x   4.1.1-2.fc38               copr_base                                       553 k
 ncurses-base                    noarch  6.3-5.20221126.fc38        copr_base                                        62 k
 ncurses-libs                    s390x   6.3-5.20221126.fc38        copr_base                                       357 k
 nettle                          s390x   3.8-2.fc38                 copr_base                                       444 k
 npth                            s390x   1.6-10.fc38                copr_base                                        24 k
 openldap                        s390x   2.6.3-1.fc38               copr_base                                       262 k
 openssl-libs                    s390x   1:3.0.5-6.fc38             copr_base                                       1.8 M
 p11-kit                         s390x   0.24.1-5.fc38              copr_base                                       370 k
 p11-kit-trust                   s390x   0.24.1-5.fc38              copr_base                                       137 k
 pcre2                           s390x   10.40-1.fc38.1             copr_base                                       251 k
 pcre2-syntax                    noarch  10.40-1.fc38.1             copr_base                                       143 k
 popt                            s390x   1.19-1.fc38                fedora                                           67 k
 publicsuffix-list-dafsa         noarch  20221208-1.fc38            fedora                                           59 k
 python-pip-wheel                noarch  22.3.1-1.fc38              fedora                                          1.4 M
 python-setuptools-wheel         noarch  65.5.1-1.fc38              fedora                                          715 k
 python3                         s390x   3.11.1-1.fc38              fedora                                           27 k
 python3-dateutil                noarch  1:2.8.2-4.fc37             fedora                                          361 k
 python3-dbus                    s390x   1.3.2-1.fc38               copr_base                                       147 k
 python3-distro                  noarch  1.8.0-1.fc38               fedora                                           49 k
 python3-dnf                     noarch  4.14.0-1.fc38              fedora                                          607 k
 python3-dnf-plugins-core        noarch  4.3.1-1.fc38               fedora                                          277 k
 python3-gpg                     s390x   1.17.1-3.fc38              copr_base                                       281 k
 python3-hawkey                  s390x   0.68.0-1.fc38              copr_base                                       105 k
 python3-libcomps                s390x   0.1.18-4.fc38              copr_base                                        50 k
 python3-libdnf                  s390x   0.68.0-1.fc38              copr_base                                       796 k
 python3-libs                    s390x   3.11.1-1.fc38              fedora                                          9.5 M
 python3-rpm                     s390x   4.18.0-8.fc38              fedora                                           95 k
 python3-six                     noarch  1.16.0-8.fc37              fedora                                           42 k
 readline                        s390x   8.2-2.fc38                 fedora                                          213 k
 rpm                             s390x   4.18.0-8.fc38              fedora                                          569 k
 rpm-build-libs                  s390x   4.18.0-8.fc38              fedora                                           92 k
 rpm-libs                        s390x   4.18.0-8.fc38              fedora                                          307 k
 rpm-sequoia                     s390x   1.2.0-1.fc38               fedora                                          960 k
 rpm-sign-libs                   s390x   4.18.0-8.fc38              fedora                                           26 k
 sed                             s390x   4.8-11.fc37                fedora                                          304 k
 setup                           noarch  2.14.3-1.fc38              fedora                                          152 k
 shadow-utils                    s390x   2:4.13-3.fc38              fedora                                          1.2 M
 sqlite-libs                     s390x   3.40.0-1.fc38              fedora                                          651 k
 systemd-libs                    s390x   252.4-598.fc38             fedora                                          591 k
 tpm2-tss                        s390x   4.0.0-0.1.rc2.fc38         fedora                                          630 k
 tzdata                          noarch  2022g-1.fc38               fedora                                          716 k
 xz-libs                         s390x   5.2.9-1.fc38               fedora                                           93 k
 zchunk-libs                     s390x   1.2.3-1.fc38               fedora                                           49 k
 zlib                            s390x   1.2.13-1.fc38              fedora                                           96 k

Transaction Summary
=========================================================================================================================
Install  137 Packages

Total download size: 56 M
Installed size: 200 M
Downloading Packages:
(1/137): alternatives-1.21-1.fc38.s390x.rpm     370 kB/s |  39 kB     00:00    
(2/137): bzip2-libs-1.0.8-12.fc38.s390x.rpm     9.4 kB/s |  47 kB     00:05    
(3/137): coreutils-9.1-8.fc38.s390x.rpm         232 kB/s | 1.1 MB     00:04    
(4/137): bash-5.2.9-3.fc38.s390x.rpm            375 kB/s | 1.8 MB     00:05    
(5/137): curl-7.87.0-1.fc38.s390x.rpm            10 MB/s | 345 kB     00:00    
(6/137): dbus-libs-1.14.4-1.fc38.s390x.rpm      8.3 MB/s | 159 kB     00:00    
(7/137): cyrus-sasl-lib-2.1.28-8.fc38.s390x.rpm  18 MB/s | 773 kB     00:00    
(8/137): elfutils-default-yama-scope-0.188-3.fc 2.0 MB/s |  16 kB     00:00    
(9/137): elfutils-libelf-0.188-3.fc38.s390x.rpm  11 MB/s | 202 kB     00:00    
(10/137): elfutils-libs-0.188-3.fc38.s390x.rpm   14 MB/s | 275 kB     00:00    
(11/137): coreutils-common-9.1-8.fc38.s390x.rpm  23 MB/s | 2.0 MB     00:00    
(12/137): expat-2.5.0-1.fc38.s390x.rpm           12 MB/s | 114 kB     00:00    
(13/137): findutils-4.9.0-2.fc38.s390x.rpm       17 MB/s | 489 kB     00:00    
(14/137): gdbm-libs-1.23-2.fc38.s390x.rpm       8.8 MB/s |  59 kB     00:00    
(15/137): file-libs-5.42-4.fc38.s390x.rpm        12 MB/s | 683 kB     00:00    
(16/137): gawk-5.1.1-4.fc38.s390x.rpm            17 MB/s | 1.0 MB     00:00    
(17/137): gmp-6.2.1-3.fc38.s390x.rpm             22 MB/s | 326 kB     00:00    
(18/137): gnutls-3.7.8-9.fc38.s390x.rpm          19 MB/s | 1.0 MB     00:00    
(19/137): glib2-2.74.1-2.fc38.s390x.rpm          24 MB/s | 2.7 MB     00:00    
(20/137): gpgme-1.17.1-3.fc38.s390x.rpm         7.4 MB/s | 219 kB     00:00    
(21/137): ima-evm-utils-1.4-6.fc38.s390x.rpm    9.6 MB/s |  63 kB     00:00    
(22/137): grep-3.8-1.fc38.s390x.rpm              21 MB/s | 290 kB     00:00    
(23/137): keyutils-libs-1.6.1-5.fc38.s390x.rpm  4.4 MB/s |  32 kB     00:00    
(24/137): gnupg2-2.3.8-1.fc38.s390x.rpm          24 MB/s | 2.6 MB     00:00    
(25/137): libacl-2.3.1-4.fc38.s390x.rpm         4.3 MB/s |  25 kB     00:00    
(26/137): json-c-0.16-3.fc38.s390x.rpm          1.9 MB/s |  43 kB     00:00    
(27/137): libarchive-3.6.1-3.fc38.s390x.rpm      24 MB/s | 426 kB     00:00    
(28/137): libassuan-2.5.5-5.fc38.s390x.rpm      3.6 MB/s |  67 kB     00:00    
(29/137): krb5-libs-1.20.1-3.fc38.s390x.rpm      18 MB/s | 735 kB     00:00    
(30/137): libattr-2.5.1-5.fc38.s390x.rpm        1.1 MB/s |  19 kB     00:00    
(31/137): libb2-0.98.1-7.fc38.s390x.rpm         1.6 MB/s |  27 kB     00:00    
(32/137): libcap-ng-0.8.3-4.fc38.s390x.rpm      4.1 MB/s |  33 kB     00:00    
(33/137): libcap-2.48-5.fc38.s390x.rpm          7.3 MB/s |  68 kB     00:00    
(34/137): libcom_err-1.46.5-3.fc38.s390x.rpm    2.4 MB/s |  26 kB     00:00    
(35/137): libcomps-0.1.18-4.fc38.s390x.rpm      6.2 MB/s |  81 kB     00:00    
(36/137): libbrotli-1.0.9-9.fc38.s390x.rpm       11 MB/s | 344 kB     00:00    
(37/137): libcurl-7.87.0-1.fc38.s390x.rpm        20 MB/s | 320 kB     00:00    
(38/137): libffi-3.4.4-1.fc38.s390x.rpm         5.2 MB/s |  36 kB     00:00    
(39/137): libevent-2.1.12-7.fc38.s390x.rpm       12 MB/s | 260 kB     00:00    
(40/137): libfsverity-1.4-8.fc38.s390x.rpm      3.4 MB/s |  20 kB     00:00    
(41/137): libdnf-0.68.0-1.fc38.s390x.rpm         23 MB/s | 653 kB     00:00    
(42/137): libidn2-2.3.4-1.fc38.s390x.rpm        9.6 MB/s | 155 kB     00:00    
(43/137): libgpg-error-1.46-1.fc38.s390x.rpm    8.7 MB/s | 225 kB     00:00    
(44/137): libksba-1.6.3-1.fc38.s390x.rpm         15 MB/s | 163 kB     00:00    
(45/137): libgcrypt-1.10.1-6.fc38.s390x.rpm      15 MB/s | 495 kB     00:00    
(46/137): libnghttp2-1.51.0-1.fc38.s390x.rpm    4.6 MB/s |  78 kB     00:00    
(47/137): libmodulemd-2.14.0-4.fc38.s390x.rpm   9.1 MB/s | 220 kB     00:00    
(48/137): libnsl2-2.0.0-4.fc38.s390x.rpm        1.7 MB/s |  30 kB     00:00    
(49/137): libpsl-0.21.1-6.fc38.s390x.rpm        9.4 MB/s |  66 kB     00:00    
(50/137): libreport-filesystem-2.17.6-1.fc38.no 2.8 MB/s |  14 kB     00:00    
(51/137): librepo-1.15.1-1.fc38.s390x.rpm        10 MB/s |  96 kB     00:00    
(52/137): libselinux-3.4-6.fc38.s390x.rpm       8.0 MB/s |  91 kB     00:00    
(53/137): libsemanage-3.4-6.fc38.s390x.rpm      8.7 MB/s | 122 kB     00:00    
(54/137): libsigsegv-2.14-3.fc38.s390x.rpm      3.7 MB/s |  27 kB     00:00    
(55/137): libsepol-3.4-4.fc38.s390x.rpm          14 MB/s | 330 kB     00:00    
(56/137): libssh-0.10.4-2.fc38.s390x.rpm         16 MB/s | 206 kB     00:00    
(57/137): libsolv-0.7.22-3.fc38.s390x.rpm        26 MB/s | 443 kB     00:00    
(58/137): libssh-config-0.10.4-2.fc38.noarch.rp 2.0 MB/s | 9.2 kB     00:00    
(59/137): libtasn1-4.19.0-1.fc38.s390x.rpm       11 MB/s |  78 kB     00:00    
(60/137): libverto-0.3.2-4.fc38.s390x.rpm       2.3 MB/s |  21 kB     00:00    
(61/137): libtirpc-1.3.3-0.fc38.s390x.rpm       4.5 MB/s |  97 kB     00:00    
(62/137): libunistring-1.0-2.fc38.s390x.rpm      22 MB/s | 552 kB     00:00    
(63/137): libxcrypt-4.4.33-5.fc38.s390x.rpm     8.9 MB/s | 125 kB     00:00    
(64/137): libyaml-0.2.5-8.fc38.s390x.rpm        8.7 MB/s |  62 kB     00:00    
(65/137): lua-libs-5.4.4-6.fc38.s390x.rpm        12 MB/s | 141 kB     00:00    
(66/137): libxml2-2.10.3-2.fc38.s390x.rpm        28 MB/s | 714 kB     00:00    
(67/137): lz4-libs-1.9.3-5.fc38.s390x.rpm       6.0 MB/s |  88 kB     00:00    
(68/137): mpdecimal-2.5.1-4.fc38.s390x.rpm       14 MB/s | 115 kB     00:00    
(69/137): ncurses-base-6.3-5.20221126.fc38.noar 7.8 MB/s |  62 kB     00:00    
(70/137): mpfr-4.1.1-2.fc38.s390x.rpm            23 MB/s | 553 kB     00:00    
(71/137): nettle-3.8-2.fc38.s390x.rpm            27 MB/s | 444 kB     00:00    
(72/137): ncurses-libs-6.3-5.20221126.fc38.s390  15 MB/s | 357 kB     00:00    
(73/137): npth-1.6-10.fc38.s390x.rpm            5.5 MB/s |  24 kB     00:00    
(74/137): openldap-2.6.3-1.fc38.s390x.rpm        19 MB/s | 262 kB     00:00    
(75/137): p11-kit-trust-0.24.1-5.fc38.s390x.rpm  16 MB/s | 137 kB     00:00    
(76/137): p11-kit-0.24.1-5.fc38.s390x.rpm        14 MB/s | 370 kB     00:00    
(77/137): pcre2-10.40-1.fc38.1.s390x.rpm         18 MB/s | 251 kB     00:00    
(78/137): pcre2-syntax-10.40-1.fc38.1.noarch.rp  11 MB/s | 143 kB     00:00    
(79/137): python3-dbus-1.3.2-1.fc38.s390x.rpm   8.4 MB/s | 147 kB     00:00    
(80/137): openssl-libs-3.0.5-6.fc38.s390x.rpm    33 MB/s | 1.8 MB     00:00    
(81/137): python3-hawkey-0.68.0-1.fc38.s390x.rp 9.6 MB/s | 105 kB     00:00    
(82/137): python3-libcomps-0.1.18-4.fc38.s390x. 6.0 MB/s |  50 kB     00:00    
(83/137): python3-gpg-1.17.1-3.fc38.s390x.rpm    12 MB/s | 281 kB     00:00    
(84/137): python3-libdnf-0.68.0-1.fc38.s390x.rp  34 MB/s | 796 kB     00:00    
(85/137): libgcc-13.0.0-0.4.fc38.s390x.rpm       62 kB/s |  66 kB     00:01    
(86/137): libgomp-13.0.0-0.4.fc38.s390x.rpm     239 kB/s | 305 kB     00:01    
(87/137): basesystem-11-14.fc37.noarch.rpm       23 kB/s | 7.0 kB     00:00    
(88/137): libstdc++-13.0.0-0.4.fc38.s390x.rpm   544 kB/s | 889 kB     00:01    
(89/137): audit-libs-3.0.9-2.fc38.s390x.rpm     163 kB/s | 114 kB     00:00    
(90/137): dnf-4.14.0-1.fc38.noarch.rpm          1.1 MB/s | 480 kB     00:00    
(91/137): crypto-policies-20221215-1.gita4c31a3 161 kB/s |  90 kB     00:00    
(92/137): dnf-data-4.14.0-1.fc38.noarch.rpm     303 kB/s |  43 kB     00:00    
(93/137): dnf-plugins-core-4.3.1-1.fc38.noarch. 244 kB/s |  34 kB     00:00    
(94/137): fedora-gpg-keys-38-0.3.noarch.rpm     885 kB/s | 125 kB     00:00    
(95/137): ca-certificates-2022.2.54-5.fc37.noar 912 kB/s | 829 kB     00:00    
(96/137): fedora-release-38-0.6.noarch.rpm       76 kB/s |  11 kB     00:00    
(97/137): fedora-release-common-38-0.6.noarch.r 151 kB/s |  21 kB     00:00    
(98/137): fedora-repos-38-0.3.noarch.rpm         73 kB/s |  10 kB     00:00    
(99/137): fedora-release-identity-basic-38-0.6.  76 kB/s |  11 kB     00:00    
(100/137): fedora-repos-rawhide-38-0.3.noarch.r  68 kB/s | 9.7 kB     00:00    
(101/137): glibc-common-2.36.9000-19.fc38.s390x 2.1 MB/s | 306 kB     00:00    
(102/137): glibc-minimal-langpack-2.36.9000-19. 215 kB/s |  30 kB     00:00    
(103/137): glibc-2.36.9000-19.fc38.s390x.rpm    3.5 MB/s | 1.6 MB     00:00    
(104/137): libblkid-2.38.1-3.fc38.s390x.rpm     730 kB/s | 103 kB     00:00    
(105/137): filesystem-3.18-2.fc37.s390x.rpm     1.9 MB/s | 1.1 MB     00:00    
(106/137): libmount-2.38.1-3.fc38.s390x.rpm     866 kB/s | 132 kB     00:00    
(107/137): libsmartcols-2.38.1-3.fc38.s390x.rpm 451 kB/s |  63 kB     00:00    
(108/137): libuuid-2.38.1-3.fc38.s390x.rpm      193 kB/s |  27 kB     00:00    
(109/137): libzstd-1.5.2-3.fc37.s390x.rpm       1.7 MB/s | 274 kB     00:00    
(110/137): popt-1.19-1.fc38.s390x.rpm           477 kB/s |  67 kB     00:00    
(111/137): publicsuffix-list-dafsa-20221208-1.f 421 kB/s |  59 kB     00:00    
(112/137): python3-3.11.1-1.fc38.s390x.rpm      193 kB/s |  27 kB     00:00    
(113/137): python-pip-wheel-22.3.1-1.fc38.noarc 4.7 MB/s | 1.4 MB     00:00    
(114/137): python-setuptools-wheel-65.5.1-1.fc3 2.5 MB/s | 715 kB     00:00    
(115/137): python3-dateutil-2.8.2-4.fc37.noarch 2.5 MB/s | 361 kB     00:00    
(116/137): python3-distro-1.8.0-1.fc38.noarch.r 326 kB/s |  49 kB     00:00    
(117/137): python3-dnf-4.14.0-1.fc38.noarch.rpm 4.1 MB/s | 607 kB     00:00    
(118/137): python3-dnf-plugins-core-4.3.1-1.fc3 1.9 MB/s | 277 kB     00:00    
(119/137): python3-rpm-4.18.0-8.fc38.s390x.rpm  677 kB/s |  95 kB     00:00    
(120/137): python3-six-1.16.0-8.fc37.noarch.rpm 300 kB/s |  42 kB     00:00    
(121/137): readline-8.2-2.fc38.s390x.rpm        1.5 MB/s | 213 kB     00:00    
(122/137): rpm-4.18.0-8.fc38.s390x.rpm          3.8 MB/s | 569 kB     00:00    
(123/137): rpm-build-libs-4.18.0-8.fc38.s390x.r 653 kB/s |  92 kB     00:00    
(124/137): rpm-libs-4.18.0-8.fc38.s390x.rpm     2.1 MB/s | 307 kB     00:00    
(125/137): rpm-sequoia-1.2.0-1.fc38.s390x.rpm   6.3 MB/s | 960 kB     00:00    
(126/137): rpm-sign-libs-4.18.0-8.fc38.s390x.rp 187 kB/s |  26 kB     00:00    
(127/137): sed-4.8-11.fc37.s390x.rpm            2.1 MB/s | 304 kB     00:00    
(128/137): setup-2.14.3-1.fc38.noarch.rpm       1.0 MB/s | 152 kB     00:00    
(129/137): shadow-utils-4.13-3.fc38.s390x.rpm   8.2 MB/s | 1.2 MB     00:00    
(130/137): sqlite-libs-3.40.0-1.fc38.s390x.rpm  4.3 MB/s | 651 kB     00:00    
(131/137): systemd-libs-252.4-598.fc38.s390x.rp 4.0 MB/s | 591 kB     00:00    
(132/137): tpm2-tss-4.0.0-0.1.rc2.fc38.s390x.rp 4.2 MB/s | 630 kB     00:00    
(133/137): python3-libs-3.11.1-1.fc38.s390x.rpm 8.8 MB/s | 9.5 MB     00:01    
(134/137): tzdata-2022g-1.fc38.noarch.rpm       4.8 MB/s | 716 kB     00:00    
(135/137): xz-libs-5.2.9-1.fc38.s390x.rpm       656 kB/s |  93 kB     00:00    
(136/137): zchunk-libs-1.2.3-1.fc38.s390x.rpm   321 kB/s |  49 kB     00:00    
(137/137): zlib-1.2.13-1.fc38.s390x.rpm         675 kB/s |  96 kB     00:00    
--------------------------------------------------------------------------------
Total                                           5.0 MB/s |  56 MB     00:11     
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
fedora                                          1.6 MB/s | 1.6 kB     00:00    
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0x5323552A:
 Userid     : "Fedora (37) <fedora-37-primary@fedoraproject.org>"
 Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.18-2.fc37.s390x                           1/1 
  Preparing        :                                                        1/1 
  Installing       : libgcc-13.0.0-0.4.fc38.s390x                         1/137 
  Running scriptlet: libgcc-13.0.0-0.4.fc38.s390x                         1/137 
  Installing       : crypto-policies-20221215-1.gita4c31a3.fc38.noarc     2/137 
  Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc     2/137 
  Installing       : tzdata-2022g-1.fc38.noarch                           3/137 
  Installing       : fedora-release-identity-basic-38-0.6.noarch          4/137 
  Installing       : python-setuptools-wheel-65.5.1-1.fc38.noarch         5/137 
  Installing       : publicsuffix-list-dafsa-20221208-1.fc38.noarch       6/137 
  Installing       : fedora-gpg-keys-38-0.3.noarch                        7/137 
  Installing       : fedora-release-38-0.6.noarch                         8/137 
  Installing       : fedora-release-common-38-0.6.noarch                  9/137 
  Installing       : fedora-repos-rawhide-38-0.3.noarch                  10/137 
  Installing       : fedora-repos-38-0.3.noarch                          11/137 
  Installing       : setup-2.14.3-1.fc38.noarch                          12/137 
  Running scriptlet: setup-2.14.3-1.fc38.noarch                          12/137 
  Installing       : filesystem-3.18-2.fc37.s390x                        13/137 
  Installing       : basesystem-11-14.fc37.noarch                        14/137 
  Installing       : pcre2-syntax-10.40-1.fc38.1.noarch                  15/137 
  Installing       : ncurses-base-6.3-5.20221126.fc38.noarch             16/137 
  Installing       : ncurses-libs-6.3-5.20221126.fc38.s390x              17/137 
  Running scriptlet: glibc-2.36.9000-19.fc38.s390x                       18/137 
  Installing       : glibc-2.36.9000-19.fc38.s390x                       18/137 
  Running scriptlet: glibc-2.36.9000-19.fc38.s390x                       18/137 
  Installing       : bash-5.2.9-3.fc38.s390x                             19/137 
  Running scriptlet: bash-5.2.9-3.fc38.s390x                             19/137 
  Installing       : glibc-common-2.36.9000-19.fc38.s390x                20/137 
  Installing       : glibc-minimal-langpack-2.36.9000-19.fc38.s390x      21/137 
  Installing       : zlib-1.2.13-1.fc38.s390x                            22/137 
  Installing       : bzip2-libs-1.0.8-12.fc38.s390x                      23/137 
  Installing       : xz-libs-5.2.9-1.fc38.s390x                          24/137 
  Installing       : libzstd-1.5.2-3.fc37.s390x                          25/137 
  Installing       : sqlite-libs-3.40.0-1.fc38.s390x                     26/137 
  Installing       : gmp-1:6.2.1-3.fc38.s390x                            27/137 
  Installing       : libcap-2.48-5.fc38.s390x                            28/137 
  Installing       : libgpg-error-1.46-1.fc38.s390x                      29/137 
  Installing       : popt-1.19-1.fc38.s390x                              30/137 
  Installing       : libxml2-2.10.3-2.fc38.s390x                         31/137 
  Installing       : lua-libs-5.4.4-6.fc38.s390x                         32/137 
  Installing       : libstdc++-13.0.0-0.4.fc38.s390x                     33/137 
  Installing       : libuuid-2.38.1-3.fc38.s390x                         34/137 
  Installing       : elfutils-libelf-0.188-3.fc38.s390x                  35/137 
  Installing       : file-libs-5.42-4.fc38.s390x                         36/137 
  Installing       : libattr-2.5.1-5.fc38.s390x                          37/137 
  Installing       : libacl-2.3.1-4.fc38.s390x                           38/137 
  Installing       : libffi-3.4.4-1.fc38.s390x                           39/137 
  Installing       : p11-kit-0.24.1-5.fc38.s390x                         40/137 
  Installing       : libunistring-1.0-2.fc38.s390x                       41/137 
  Installing       : libidn2-2.3.4-1.fc38.s390x                          42/137 
  Installing       : libxcrypt-4.4.33-5.fc38.s390x                       43/137 
  Installing       : pcre2-10.40-1.fc38.1.s390x                          44/137 
  Installing       : readline-8.2-2.fc38.s390x                           45/137 
  Installing       : libassuan-2.5.5-5.fc38.s390x                        46/137 
  Installing       : nettle-3.8-2.fc38.s390x                             47/137 
  Installing       : rpm-sequoia-1.2.0-1.fc38.s390x                      48/137 
  Installing       : expat-2.5.0-1.fc38.s390x                            49/137 
  Installing       : gdbm-libs-1:1.23-2.fc38.s390x                       50/137 
  Installing       : json-c-0.16-3.fc38.s390x                            51/137 
  Installing       : keyutils-libs-1.6.1-5.fc38.s390x                    52/137 
  Installing       : libcom_err-1.46.5-3.fc38.s390x                      53/137 
  Installing       : libsepol-3.4-4.fc38.s390x                           54/137 
  Installing       : libselinux-3.4-6.fc38.s390x                         55/137 
  Installing       : sed-4.8-11.fc37.s390x                               56/137 
  Installing       : libtasn1-4.19.0-1.fc38.s390x                        57/137 
  Installing       : lz4-libs-1.9.3-5.fc38.s390x                         58/137 
  Installing       : libgomp-13.0.0-0.4.fc38.s390x                       59/137 
  Installing       : libsmartcols-2.38.1-3.fc38.s390x                    60/137 
  Installing       : libb2-0.98.1-7.fc38.s390x                           61/137 
  Installing       : systemd-libs-252.4-598.fc38.s390x                   62/137 
  Installing       : dbus-libs-1:1.14.4-1.fc38.s390x                     63/137 
  Installing       : findutils-1:4.9.0-2.fc38.s390x                      64/137 
  Installing       : cyrus-sasl-lib-2.1.28-8.fc38.s390x                  65/137 
  Installing       : libcomps-0.1.18-4.fc38.s390x                        66/137 
  Installing       : grep-3.8-1.fc38.s390x                               67/137 
  Installing       : libpsl-0.21.1-6.fc38.s390x                          68/137 
  Installing       : libblkid-2.38.1-3.fc38.s390x                        69/137 
  Installing       : libmount-2.38.1-3.fc38.s390x                        70/137 
  Installing       : mpdecimal-2.5.1-4.fc38.s390x                        71/137 
  Installing       : libgcrypt-1.10.1-6.fc38.s390x                       72/137 
  Installing       : libksba-1.6.3-1.fc38.s390x                          73/137 
  Installing       : mpfr-4.1.1-2.fc38.s390x                             74/137 
  Installing       : elfutils-default-yama-scope-0.188-3.fc38.noarch     75/137 
  Running scriptlet: elfutils-default-yama-scope-0.188-3.fc38.noarch     75/137 
  Installing       : elfutils-libs-0.188-3.fc38.s390x                    76/137 
  Installing       : alternatives-1.21-1.fc38.s390x                      77/137 
  Installing       : p11-kit-trust-0.24.1-5.fc38.s390x                   78/137 
  Running scriptlet: p11-kit-trust-0.24.1-5.fc38.s390x                   78/137 
  Installing       : gnutls-3.7.8-9.fc38.s390x                           79/137 
  Installing       : glib2-2.74.1-2.fc38.s390x                           80/137 
  Installing       : libbrotli-1.0.9-9.fc38.s390x                        81/137 
  Installing       : libcap-ng-0.8.3-4.fc38.s390x                        82/137 
  Installing       : audit-libs-3.0.9-2.fc38.s390x                       83/137 
  Installing       : rpm-libs-4.18.0-8.fc38.s390x                        84/137 
  Installing       : rpm-build-libs-4.18.0-8.fc38.s390x                  85/137 
  Installing       : libsemanage-3.4-6.fc38.s390x                        86/137 
  Installing       : shadow-utils-2:4.13-3.fc38.s390x                    87/137 
  Installing       : libnghttp2-1.51.0-1.fc38.s390x                      88/137 
  Installing       : libsigsegv-2.14-3.fc38.s390x                        89/137 
  Installing       : gawk-5.1.1-4.fc38.s390x                             90/137 
  Installing       : libverto-0.3.2-4.fc38.s390x                         91/137 
  Installing       : libyaml-0.2.5-8.fc38.s390x                          92/137 
  Installing       : libmodulemd-2.14.0-4.fc38.s390x                     93/137 
  Installing       : npth-1.6-10.fc38.s390x                              94/137 
  Installing       : libssh-config-0.10.4-2.fc38.noarch                  95/137 
  Installing       : libreport-filesystem-2.17.6-1.fc38.noarch           96/137 
  Installing       : dnf-data-4.14.0-1.fc38.noarch                       97/137 
warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew

  Installing       : coreutils-common-9.1-8.fc38.s390x                   98/137 
  Installing       : openssl-libs-1:3.0.5-6.fc38.s390x                   99/137 
  Installing       : coreutils-9.1-8.fc38.s390x                         100/137 
  Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch            101/137 
  Installing       : ca-certificates-2022.2.54-5.fc37.noarch            101/137 
  Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch            101/137 
  Installing       : krb5-libs-1.20.1-3.fc38.s390x                      102/137 
  Installing       : libtirpc-1.3.3-0.fc38.s390x                        103/137 
  Installing       : libfsverity-1.4-8.fc38.s390x                       104/137 
  Installing       : zchunk-libs-1.2.3-1.fc38.s390x                     105/137 
  Installing       : libsolv-0.7.22-3.fc38.s390x                        106/137 
  Installing       : libnsl2-2.0.0-4.fc38.s390x                         107/137 
  Installing       : libssh-0.10.4-2.fc38.s390x                         108/137 
  Installing       : python-pip-wheel-22.3.1-1.fc38.noarch              109/137 
  Installing       : python3-3.11.1-1.fc38.s390x                        110/137 
  Installing       : python3-libs-3.11.1-1.fc38.s390x                   111/137 
  Installing       : python3-dbus-1.3.2-1.fc38.s390x                    112/137 
  Installing       : python3-libcomps-0.1.18-4.fc38.s390x               113/137 
  Installing       : python3-distro-1.8.0-1.fc38.noarch                 114/137 
  Installing       : python3-six-1.16.0-8.fc37.noarch                   115/137 
  Installing       : python3-dateutil-1:2.8.2-4.fc37.noarch             116/137 
  Installing       : libarchive-3.6.1-3.fc38.s390x                      117/137 
  Installing       : libevent-2.1.12-7.fc38.s390x                       118/137 
  Installing       : openldap-2.6.3-1.fc38.s390x                        119/137 
  Installing       : libcurl-7.87.0-1.fc38.s390x                        120/137 
  Installing       : gnupg2-2.3.8-1.fc38.s390x                          121/137 
  Installing       : gpgme-1.17.1-3.fc38.s390x                          122/137 
  Installing       : librepo-1.15.1-1.fc38.s390x                        123/137 
  Installing       : libdnf-0.68.0-1.fc38.s390x                         124/137 
  Installing       : python3-libdnf-0.68.0-1.fc38.s390x                 125/137 
  Installing       : python3-hawkey-0.68.0-1.fc38.s390x                 126/137 
  Installing       : python3-gpg-1.17.1-3.fc38.s390x                    127/137 
  Installing       : curl-7.87.0-1.fc38.s390x                           128/137 
  Running scriptlet: tpm2-tss-4.0.0-0.1.rc2.fc38.s390x                  129/137 
useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'

  Installing       : tpm2-tss-4.0.0-0.1.rc2.fc38.s390x                  129/137 
  Installing       : ima-evm-utils-1.4-6.fc38.s390x                     130/137 
  Installing       : rpm-sign-libs-4.18.0-8.fc38.s390x                  131/137 
  Installing       : python3-rpm-4.18.0-8.fc38.s390x                    132/137 
  Installing       : python3-dnf-4.14.0-1.fc38.noarch                   133/137 
  Installing       : python3-dnf-plugins-core-4.3.1-1.fc38.noarch       134/137 
  Installing       : dnf-plugins-core-4.3.1-1.fc38.noarch               135/137 
  Installing       : dnf-4.14.0-1.fc38.noarch                           136/137 
  Running scriptlet: dnf-4.14.0-1.fc38.noarch                           136/137 
  Running scriptlet: rpm-4.18.0-8.fc38.s390x                            137/137 
  Installing       : rpm-4.18.0-8.fc38.s390x                            137/137 
  Running scriptlet: filesystem-3.18-2.fc37.s390x                       137/137 
  Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch            137/137 
  Running scriptlet: rpm-4.18.0-8.fc38.s390x                            137/137 
  Verifying        : alternatives-1.21-1.fc38.s390x                       1/137 
  Verifying        : bash-5.2.9-3.fc38.s390x                              2/137 
  Verifying        : bzip2-libs-1.0.8-12.fc38.s390x                       3/137 
  Verifying        : coreutils-9.1-8.fc38.s390x                           4/137 
  Verifying        : coreutils-common-9.1-8.fc38.s390x                    5/137 
  Verifying        : curl-7.87.0-1.fc38.s390x                             6/137 
  Verifying        : cyrus-sasl-lib-2.1.28-8.fc38.s390x                   7/137 
  Verifying        : dbus-libs-1:1.14.4-1.fc38.s390x                      8/137 
  Verifying        : elfutils-default-yama-scope-0.188-3.fc38.noarch      9/137 
  Verifying        : elfutils-libelf-0.188-3.fc38.s390x                  10/137 
  Verifying        : elfutils-libs-0.188-3.fc38.s390x                    11/137 
  Verifying        : expat-2.5.0-1.fc38.s390x                            12/137 
  Verifying        : file-libs-5.42-4.fc38.s390x                         13/137 
  Verifying        : findutils-1:4.9.0-2.fc38.s390x                      14/137 
  Verifying        : gawk-5.1.1-4.fc38.s390x                             15/137 
  Verifying        : gdbm-libs-1:1.23-2.fc38.s390x                       16/137 
  Verifying        : glib2-2.74.1-2.fc38.s390x                           17/137 
  Verifying        : gmp-1:6.2.1-3.fc38.s390x                            18/137 
  Verifying        : gnupg2-2.3.8-1.fc38.s390x                           19/137 
  Verifying        : gnutls-3.7.8-9.fc38.s390x                           20/137 
  Verifying        : gpgme-1.17.1-3.fc38.s390x                           21/137 
  Verifying        : grep-3.8-1.fc38.s390x                               22/137 
  Verifying        : ima-evm-utils-1.4-6.fc38.s390x                      23/137 
  Verifying        : json-c-0.16-3.fc38.s390x                            24/137 
  Verifying        : keyutils-libs-1.6.1-5.fc38.s390x                    25/137 
  Verifying        : krb5-libs-1.20.1-3.fc38.s390x                       26/137 
  Verifying        : libacl-2.3.1-4.fc38.s390x                           27/137 
  Verifying        : libarchive-3.6.1-3.fc38.s390x                       28/137 
  Verifying        : libassuan-2.5.5-5.fc38.s390x                        29/137 
  Verifying        : libattr-2.5.1-5.fc38.s390x                          30/137 
  Verifying        : libb2-0.98.1-7.fc38.s390x                           31/137 
  Verifying        : libbrotli-1.0.9-9.fc38.s390x                        32/137 
  Verifying        : libcap-2.48-5.fc38.s390x                            33/137 
  Verifying        : libcap-ng-0.8.3-4.fc38.s390x                        34/137 
  Verifying        : libcom_err-1.46.5-3.fc38.s390x                      35/137 
  Verifying        : libcomps-0.1.18-4.fc38.s390x                        36/137 
  Verifying        : libcurl-7.87.0-1.fc38.s390x                         37/137 
  Verifying        : libdnf-0.68.0-1.fc38.s390x                          38/137 
  Verifying        : libevent-2.1.12-7.fc38.s390x                        39/137 
  Verifying        : libffi-3.4.4-1.fc38.s390x                           40/137 
  Verifying        : libfsverity-1.4-8.fc38.s390x                        41/137 
  Verifying        : libgcrypt-1.10.1-6.fc38.s390x                       42/137 
  Verifying        : libgpg-error-1.46-1.fc38.s390x                      43/137 
  Verifying        : libidn2-2.3.4-1.fc38.s390x                          44/137 
  Verifying        : libksba-1.6.3-1.fc38.s390x                          45/137 
  Verifying        : libmodulemd-2.14.0-4.fc38.s390x                     46/137 
  Verifying        : libnghttp2-1.51.0-1.fc38.s390x                      47/137 
  Verifying        : libnsl2-2.0.0-4.fc38.s390x                          48/137 
  Verifying        : libpsl-0.21.1-6.fc38.s390x                          49/137 
  Verifying        : librepo-1.15.1-1.fc38.s390x                         50/137 
  Verifying        : libreport-filesystem-2.17.6-1.fc38.noarch           51/137 
  Verifying        : libselinux-3.4-6.fc38.s390x                         52/137 
  Verifying        : libsemanage-3.4-6.fc38.s390x                        53/137 
  Verifying        : libsepol-3.4-4.fc38.s390x                           54/137 
  Verifying        : libsigsegv-2.14-3.fc38.s390x                        55/137 
  Verifying        : libsolv-0.7.22-3.fc38.s390x                         56/137 
  Verifying        : libssh-0.10.4-2.fc38.s390x                          57/137 
  Verifying        : libssh-config-0.10.4-2.fc38.noarch                  58/137 
  Verifying        : libtasn1-4.19.0-1.fc38.s390x                        59/137 
  Verifying        : libtirpc-1.3.3-0.fc38.s390x                         60/137 
  Verifying        : libunistring-1.0-2.fc38.s390x                       61/137 
  Verifying        : libverto-0.3.2-4.fc38.s390x                         62/137 
  Verifying        : libxcrypt-4.4.33-5.fc38.s390x                       63/137 
  Verifying        : libxml2-2.10.3-2.fc38.s390x                         64/137 
  Verifying        : libyaml-0.2.5-8.fc38.s390x                          65/137 
  Verifying        : lua-libs-5.4.4-6.fc38.s390x                         66/137 
  Verifying        : lz4-libs-1.9.3-5.fc38.s390x                         67/137 
  Verifying        : mpdecimal-2.5.1-4.fc38.s390x                        68/137 
  Verifying        : mpfr-4.1.1-2.fc38.s390x                             69/137 
  Verifying        : ncurses-base-6.3-5.20221126.fc38.noarch             70/137 
  Verifying        : ncurses-libs-6.3-5.20221126.fc38.s390x              71/137 
  Verifying        : nettle-3.8-2.fc38.s390x                             72/137 
  Verifying        : npth-1.6-10.fc38.s390x                              73/137 
  Verifying        : openldap-2.6.3-1.fc38.s390x                         74/137 
  Verifying        : openssl-libs-1:3.0.5-6.fc38.s390x                   75/137 
  Verifying        : p11-kit-0.24.1-5.fc38.s390x                         76/137 
  Verifying        : p11-kit-trust-0.24.1-5.fc38.s390x                   77/137 
  Verifying        : pcre2-10.40-1.fc38.1.s390x                          78/137 
  Verifying        : pcre2-syntax-10.40-1.fc38.1.noarch                  79/137 
  Verifying        : python3-dbus-1.3.2-1.fc38.s390x                     80/137 
  Verifying        : python3-gpg-1.17.1-3.fc38.s390x                     81/137 
  Verifying        : python3-hawkey-0.68.0-1.fc38.s390x                  82/137 
  Verifying        : python3-libcomps-0.1.18-4.fc38.s390x                83/137 
  Verifying        : python3-libdnf-0.68.0-1.fc38.s390x                  84/137 
  Verifying        : libgcc-13.0.0-0.4.fc38.s390x                        85/137 
  Verifying        : libgomp-13.0.0-0.4.fc38.s390x                       86/137 
  Verifying        : libstdc++-13.0.0-0.4.fc38.s390x                     87/137 
  Verifying        : audit-libs-3.0.9-2.fc38.s390x                       88/137 
  Verifying        : basesystem-11-14.fc37.noarch                        89/137 
  Verifying        : ca-certificates-2022.2.54-5.fc37.noarch             90/137 
  Verifying        : crypto-policies-20221215-1.gita4c31a3.fc38.noarc    91/137 
  Verifying        : dnf-4.14.0-1.fc38.noarch                            92/137 
  Verifying        : dnf-data-4.14.0-1.fc38.noarch                       93/137 
  Verifying        : dnf-plugins-core-4.3.1-1.fc38.noarch                94/137 
  Verifying        : fedora-gpg-keys-38-0.3.noarch                       95/137 
  Verifying        : fedora-release-38-0.6.noarch                        96/137 
  Verifying        : fedora-release-common-38-0.6.noarch                 97/137 
  Verifying        : fedora-release-identity-basic-38-0.6.noarch         98/137 
  Verifying        : fedora-repos-38-0.3.noarch                          99/137 
  Verifying        : fedora-repos-rawhide-38-0.3.noarch                 100/137 
  Verifying        : filesystem-3.18-2.fc37.s390x                       101/137 
  Verifying        : glibc-2.36.9000-19.fc38.s390x                      102/137 
  Verifying        : glibc-common-2.36.9000-19.fc38.s390x               103/137 
  Verifying        : glibc-minimal-langpack-2.36.9000-19.fc38.s390x     104/137 
  Verifying        : libblkid-2.38.1-3.fc38.s390x                       105/137 
  Verifying        : libmount-2.38.1-3.fc38.s390x                       106/137 
  Verifying        : libsmartcols-2.38.1-3.fc38.s390x                   107/137 
  Verifying        : libuuid-2.38.1-3.fc38.s390x                        108/137 
  Verifying        : libzstd-1.5.2-3.fc37.s390x                         109/137 
  Verifying        : popt-1.19-1.fc38.s390x                             110/137 
  Verifying        : publicsuffix-list-dafsa-20221208-1.fc38.noarch     111/137 
  Verifying        : python-pip-wheel-22.3.1-1.fc38.noarch              112/137 
  Verifying        : python-setuptools-wheel-65.5.1-1.fc38.noarch       113/137 
  Verifying        : python3-3.11.1-1.fc38.s390x                        114/137 
  Verifying        : python3-dateutil-1:2.8.2-4.fc37.noarch             115/137 
  Verifying        : python3-distro-1.8.0-1.fc38.noarch                 116/137 
  Verifying        : python3-dnf-4.14.0-1.fc38.noarch                   117/137 
  Verifying        : python3-dnf-plugins-core-4.3.1-1.fc38.noarch       118/137 
  Verifying        : python3-libs-3.11.1-1.fc38.s390x                   119/137 
  Verifying        : python3-rpm-4.18.0-8.fc38.s390x                    120/137 
  Verifying        : python3-six-1.16.0-8.fc37.noarch                   121/137 
  Verifying        : readline-8.2-2.fc38.s390x                          122/137 
  Verifying        : rpm-4.18.0-8.fc38.s390x                            123/137 
  Verifying        : rpm-build-libs-4.18.0-8.fc38.s390x                 124/137 
  Verifying        : rpm-libs-4.18.0-8.fc38.s390x                       125/137 
  Verifying        : rpm-sequoia-1.2.0-1.fc38.s390x                     126/137 
  Verifying        : rpm-sign-libs-4.18.0-8.fc38.s390x                  127/137 
  Verifying        : sed-4.8-11.fc37.s390x                              128/137 
  Verifying        : setup-2.14.3-1.fc38.noarch                         129/137 
  Verifying        : shadow-utils-2:4.13-3.fc38.s390x                   130/137 
  Verifying        : sqlite-libs-3.40.0-1.fc38.s390x                    131/137 
  Verifying        : systemd-libs-252.4-598.fc38.s390x                  132/137 
  Verifying        : tpm2-tss-4.0.0-0.1.rc2.fc38.s390x                  133/137 
  Verifying        : tzdata-2022g-1.fc38.noarch                         134/137 
  Verifying        : xz-libs-5.2.9-1.fc38.s390x                         135/137 
  Verifying        : zchunk-libs-1.2.3-1.fc38.s390x                     136/137 
  Verifying        : zlib-1.2.13-1.fc38.s390x                           137/137 
Installed products updated.

Installed:
  alternatives-1.21-1.fc38.s390x                                                
  audit-libs-3.0.9-2.fc38.s390x                                                 
  basesystem-11-14.fc37.noarch                                                  
  bash-5.2.9-3.fc38.s390x                                                       
  bzip2-libs-1.0.8-12.fc38.s390x                                                
  ca-certificates-2022.2.54-5.fc37.noarch                                       
  coreutils-9.1-8.fc38.s390x                                                    
  coreutils-common-9.1-8.fc38.s390x                                             
  crypto-policies-20221215-1.gita4c31a3.fc38.noarch                             
  curl-7.87.0-1.fc38.s390x                                                      
  cyrus-sasl-lib-2.1.28-8.fc38.s390x                                            
  dbus-libs-1:1.14.4-1.fc38.s390x                                               
  dnf-4.14.0-1.fc38.noarch                                                      
  dnf-data-4.14.0-1.fc38.noarch                                                 
  dnf-plugins-core-4.3.1-1.fc38.noarch                                          
  elfutils-default-yama-scope-0.188-3.fc38.noarch                               
  elfutils-libelf-0.188-3.fc38.s390x                                            
  elfutils-libs-0.188-3.fc38.s390x                                              
  expat-2.5.0-1.fc38.s390x                                                      
  fedora-gpg-keys-38-0.3.noarch                                                 
  fedora-release-38-0.6.noarch                                                  
  fedora-release-common-38-0.6.noarch                                           
  fedora-release-identity-basic-38-0.6.noarch                                   
  fedora-repos-38-0.3.noarch                                                    
  fedora-repos-rawhide-38-0.3.noarch                                            
  file-libs-5.42-4.fc38.s390x                                                   
  filesystem-3.18-2.fc37.s390x                                                  
  findutils-1:4.9.0-2.fc38.s390x                                                
  gawk-5.1.1-4.fc38.s390x                                                       
  gdbm-libs-1:1.23-2.fc38.s390x                                                 
  glib2-2.74.1-2.fc38.s390x                                                     
  glibc-2.36.9000-19.fc38.s390x                                                 
  glibc-common-2.36.9000-19.fc38.s390x                                          
  glibc-minimal-langpack-2.36.9000-19.fc38.s390x                                
  gmp-1:6.2.1-3.fc38.s390x                                                      
  gnupg2-2.3.8-1.fc38.s390x                                                     
  gnutls-3.7.8-9.fc38.s390x                                                     
  gpgme-1.17.1-3.fc38.s390x                                                     
  grep-3.8-1.fc38.s390x                                                         
  ima-evm-utils-1.4-6.fc38.s390x                                                
  json-c-0.16-3.fc38.s390x                                                      
  keyutils-libs-1.6.1-5.fc38.s390x                                              
  krb5-libs-1.20.1-3.fc38.s390x                                                 
  libacl-2.3.1-4.fc38.s390x                                                     
  libarchive-3.6.1-3.fc38.s390x                                                 
  libassuan-2.5.5-5.fc38.s390x                                                  
  libattr-2.5.1-5.fc38.s390x                                                    
  libb2-0.98.1-7.fc38.s390x                                                     
  libblkid-2.38.1-3.fc38.s390x                                                  
  libbrotli-1.0.9-9.fc38.s390x                                                  
  libcap-2.48-5.fc38.s390x                                                      
  libcap-ng-0.8.3-4.fc38.s390x                                                  
  libcom_err-1.46.5-3.fc38.s390x                                                
  libcomps-0.1.18-4.fc38.s390x                                                  
  libcurl-7.87.0-1.fc38.s390x                                                   
  libdnf-0.68.0-1.fc38.s390x                                                    
  libevent-2.1.12-7.fc38.s390x                                                  
  libffi-3.4.4-1.fc38.s390x                                                     
  libfsverity-1.4-8.fc38.s390x                                                  
  libgcc-13.0.0-0.4.fc38.s390x                                                  
  libgcrypt-1.10.1-6.fc38.s390x                                                 
  libgomp-13.0.0-0.4.fc38.s390x                                                 
  libgpg-error-1.46-1.fc38.s390x                                                
  libidn2-2.3.4-1.fc38.s390x                                                    
  libksba-1.6.3-1.fc38.s390x                                                    
  libmodulemd-2.14.0-4.fc38.s390x                                               
  libmount-2.38.1-3.fc38.s390x                                                  
  libnghttp2-1.51.0-1.fc38.s390x                                                
  libnsl2-2.0.0-4.fc38.s390x                                                    
  libpsl-0.21.1-6.fc38.s390x                                                    
  librepo-1.15.1-1.fc38.s390x                                                   
  libreport-filesystem-2.17.6-1.fc38.noarch                                     
  libselinux-3.4-6.fc38.s390x                                                   
  libsemanage-3.4-6.fc38.s390x                                                  
  libsepol-3.4-4.fc38.s390x                                                     
  libsigsegv-2.14-3.fc38.s390x                                                  
  libsmartcols-2.38.1-3.fc38.s390x                                              
  libsolv-0.7.22-3.fc38.s390x                                                   
  libssh-0.10.4-2.fc38.s390x                                                    
  libssh-config-0.10.4-2.fc38.noarch                                            
  libstdc++-13.0.0-0.4.fc38.s390x                                               
  libtasn1-4.19.0-1.fc38.s390x                                                  
  libtirpc-1.3.3-0.fc38.s390x                                                   
  libunistring-1.0-2.fc38.s390x                                                 
  libuuid-2.38.1-3.fc38.s390x                                                   
  libverto-0.3.2-4.fc38.s390x                                                   
  libxcrypt-4.4.33-5.fc38.s390x                                                 
  libxml2-2.10.3-2.fc38.s390x                                                   
  libyaml-0.2.5-8.fc38.s390x                                                    
  libzstd-1.5.2-3.fc37.s390x                                                    
  lua-libs-5.4.4-6.fc38.s390x                                                   
  lz4-libs-1.9.3-5.fc38.s390x                                                   
  mpdecimal-2.5.1-4.fc38.s390x                                                  
  mpfr-4.1.1-2.fc38.s390x                                                       
  ncurses-base-6.3-5.20221126.fc38.noarch                                       
  ncurses-libs-6.3-5.20221126.fc38.s390x                                        
  nettle-3.8-2.fc38.s390x                                                       
  npth-1.6-10.fc38.s390x                                                        
  openldap-2.6.3-1.fc38.s390x                                                   
  openssl-libs-1:3.0.5-6.fc38.s390x                                             
  p11-kit-0.24.1-5.fc38.s390x                                                   
  p11-kit-trust-0.24.1-5.fc38.s390x                                             
  pcre2-10.40-1.fc38.1.s390x                                                    
  pcre2-syntax-10.40-1.fc38.1.noarch                                            
  popt-1.19-1.fc38.s390x                                                        
  publicsuffix-list-dafsa-20221208-1.fc38.noarch                                
  python-pip-wheel-22.3.1-1.fc38.noarch                                         
  python-setuptools-wheel-65.5.1-1.fc38.noarch                                  
  python3-3.11.1-1.fc38.s390x                                                   
  python3-dateutil-1:2.8.2-4.fc37.noarch                                        
  python3-dbus-1.3.2-1.fc38.s390x                                               
  python3-distro-1.8.0-1.fc38.noarch                                            
  python3-dnf-4.14.0-1.fc38.noarch                                              
  python3-dnf-plugins-core-4.3.1-1.fc38.noarch                                  
  python3-gpg-1.17.1-3.fc38.s390x                                               
  python3-hawkey-0.68.0-1.fc38.s390x                                            
  python3-libcomps-0.1.18-4.fc38.s390x                                          
  python3-libdnf-0.68.0-1.fc38.s390x                                            
  python3-libs-3.11.1-1.fc38.s390x                                              
  python3-rpm-4.18.0-8.fc38.s390x                                               
  python3-six-1.16.0-8.fc37.noarch                                              
  readline-8.2-2.fc38.s390x                                                     
  rpm-4.18.0-8.fc38.s390x                                                       
  rpm-build-libs-4.18.0-8.fc38.s390x                                            
  rpm-libs-4.18.0-8.fc38.s390x                                                  
  rpm-sequoia-1.2.0-1.fc38.s390x                                                
  rpm-sign-libs-4.18.0-8.fc38.s390x                                             
  sed-4.8-11.fc37.s390x                                                         
  setup-2.14.3-1.fc38.noarch                                                    
  shadow-utils-2:4.13-3.fc38.s390x                                              
  sqlite-libs-3.40.0-1.fc38.s390x                                               
  systemd-libs-252.4-598.fc38.s390x                                             
  tpm2-tss-4.0.0-0.1.rc2.fc38.s390x                                             
  tzdata-2022g-1.fc38.noarch                                                    
  xz-libs-5.2.9-1.fc38.s390x                                                    
  zchunk-libs-1.2.3-1.fc38.s390x                                                
  zlib-1.2.13-1.fc38.s390x                                                      

Complete!
Finish(bootstrap): dnf install
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1672058577.895426/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                                 552  B/s | 3.0 kB     00:05    
Copr repository                                 4.9 MB/s |  29 MB     00:05    
Additional repo https_jakub_fedorapeople_org_fe 1.9 kB/s | 3.0 kB     00:01    
fedora                                          6.9 kB/s | 6.6 kB     00:00    
Dependencies resolved.
=========================================================================================================================
 Package                         Arch    Version                    Repository                                       Size
=========================================================================================================================
Installing group/module packages:
 bash                            s390x   5.2.9-3.fc38               copr_base                                       1.8 M
 bzip2                           s390x   1.0.8-12.fc38              copr_base                                        54 k
 coreutils                       s390x   9.1-8.fc38                 copr_base                                       1.1 M
 cpio                            s390x   2.13-13.fc38               copr_base                                       275 k
 diffutils                       s390x   3.8-3.fc38                 copr_base                                       381 k
 fedora-release-common           noarch  38-0.6                     fedora                                           21 k
 findutils                       s390x   1:4.9.0-2.fc38             copr_base                                       489 k
 gawk                            s390x   5.1.1-4.fc38               copr_base                                       1.0 M
 glibc-minimal-langpack          s390x   2.36.9000-19.fc38          fedora                                           30 k
 grep                            s390x   3.8-1.fc38                 copr_base                                       290 k
 gzip                            s390x   1.12-2.fc38                copr_base                                       165 k
 info                            s390x   7.0.1-1.fc38               fedora                                          180 k
 patch                           s390x   2.7.6-17.fc38              copr_base                                       134 k
 redhat-rpm-config               noarch  235-1.fc38                 fedora                                           80 k
 rpm-build                       s390x   4.18.0-8.fc38              fedora                                           76 k
 sed                             s390x   4.8-11.fc37                fedora                                          304 k
 shadow-utils                    s390x   2:4.13-3.fc38              fedora                                          1.2 M
 tar                             s390x   2:1.34-5.fc38              fedora                                          876 k
 unzip                           s390x   6.0-58.fc38                fedora                                          177 k
 util-linux                      s390x   2.38.1-3.fc38              fedora                                          2.3 M
 which                           s390x   2.21-36.fc38               fedora                                           42 k
 xz                              s390x   5.2.9-1.fc38               fedora                                          306 k
Installing dependencies:
 alternatives                    s390x   1.21-1.fc38                copr_base                                        39 k
 ansible-srpm-macros             noarch  1-8.1.fc38                 fedora                                          8.6 k
 audit-libs                      s390x   3.0.9-2.fc38               fedora                                          114 k
 authselect                      s390x   1.4.2-1.fc38               copr_base                                       139 k
 authselect-libs                 s390x   1.4.2-1.fc38               copr_base                                       235 k
 basesystem                      noarch  11-14.fc37                 fedora                                          7.0 k
 binutils                        s390x   2.39-6.fc38                copr_base                                       5.7 M
 binutils-gold                   s390x   2.39-6.fc38                copr_base                                       994 k
 bzip2-libs                      s390x   1.0.8-12.fc38              copr_base                                        47 k
 ca-certificates                 noarch  2022.2.54-5.fc37           fedora                                          829 k
 coreutils-common                s390x   9.1-8.fc38                 copr_base                                       2.0 M
 cracklib                        s390x   2.9.7-30.fc38              copr_base                                        82 k
 crypto-policies                 noarch  20221215-1.gita4c31a3.fc38 fedora                                           90 k
 curl                            s390x   7.87.0-1.fc38              copr_base                                       345 k
 cyrus-sasl-lib                  s390x   2.1.28-8.fc38              copr_base                                       773 k
 debugedit                       s390x   5.0-5.fc37                 fedora                                           76 k
 dwz                             s390x   0.15-1.fc38                copr_base                                       144 k
 ed                              s390x   1.18-2.fc38                copr_base                                        80 k
 efi-srpm-macros                 noarch  5-6.fc37                   fedora                                           22 k
 elfutils                        s390x   0.188-3.fc38               copr_base                                       547 k
 elfutils-debuginfod-client      s390x   0.188-3.fc38               copr_base                                        41 k
 elfutils-default-yama-scope     noarch  0.188-3.fc38               copr_base                                        16 k
 elfutils-libelf                 s390x   0.188-3.fc38               copr_base                                       202 k
 elfutils-libs                   s390x   0.188-3.fc38               copr_base                                       275 k
 fedora-gpg-keys                 noarch  38-0.3                     fedora                                          125 k
 fedora-release                  noarch  38-0.6                     fedora                                           11 k
 fedora-release-identity-basic   noarch  38-0.6                     fedora                                           11 k
 fedora-repos                    noarch  38-0.3                     fedora                                           10 k
 fedora-repos-rawhide            noarch  38-0.3                     fedora                                          9.7 k
 file                            s390x   5.42-4.fc38                copr_base                                        49 k
 file-libs                       s390x   5.42-4.fc38                copr_base                                       683 k
 filesystem                      s390x   3.18-2.fc37                fedora                                          1.1 M
 fonts-srpm-macros               noarch  1:2.0.5-10.fc38            fedora                                           26 k
 fpc-srpm-macros                 noarch  1.3-6.fc37                 fedora                                          7.7 k
 gdb-minimal                     s390x   12.1-10.fc38               fedora                                          3.3 M
 gdbm-libs                       s390x   1:1.23-2.fc38              copr_base                                        59 k
 ghc-srpm-macros                 noarch  1.5.0-7.fc37               fedora                                          7.8 k
 glibc                           s390x   2.36.9000-19.fc38          fedora                                          1.6 M
 glibc-common                    s390x   2.36.9000-19.fc38          fedora                                          306 k
 glibc-gconv-extra               s390x   2.36.9000-19.fc38          fedora                                          1.6 M
 gmp                             s390x   1:6.2.1-3.fc38             copr_base                                       326 k
 gnat-srpm-macros                noarch  4-16.fc37                  fedora                                          8.3 k
 go-srpm-macros                  noarch  3.2.0-1.fc38               fedora                                           27 k
 jansson                         s390x   2.13.1-5.fc38              copr_base                                        45 k
 kernel-srpm-macros              noarch  1.0-15.fc37                fedora                                          9.4 k
 keyutils-libs                   s390x   1.6.1-5.fc38               copr_base                                        32 k
 krb5-libs                       s390x   1.20.1-3.fc38              copr_base                                       735 k
 libacl                          s390x   2.3.1-4.fc38               copr_base                                        25 k
 libarchive                      s390x   3.6.1-3.fc38               copr_base                                       426 k
 libattr                         s390x   2.5.1-5.fc38               copr_base                                        19 k
 libblkid                        s390x   2.38.1-3.fc38              fedora                                          103 k
 libbrotli                       s390x   1.0.9-9.fc38               copr_base                                       344 k
 libcap                          s390x   2.48-5.fc38                copr_base                                        68 k
 libcap-ng                       s390x   0.8.3-4.fc38               copr_base                                        33 k
 libcom_err                      s390x   1.46.5-3.fc38              copr_base                                        26 k
 libcurl                         s390x   7.87.0-1.fc38              copr_base                                       320 k
 libdb                           s390x   5.3.28-54.fc38             copr_base                                       775 k
 libeconf                        s390x   0.4.0-4.fc38               copr_base                                        29 k
 libevent                        s390x   2.1.12-7.fc38              copr_base                                       260 k
 libfdisk                        s390x   2.38.1-3.fc38              fedora                                          156 k
 libffi                          s390x   3.4.4-1.fc38               copr_base                                        36 k
 libgcc                          s390x   13.0.0-0.4.fc38            https_jakub_fedorapeople_org_fedora_gcc13_arch   66 k
 libgomp                         s390x   13.0.0-0.4.fc38            https_jakub_fedorapeople_org_fedora_gcc13_arch  305 k
 libidn2                         s390x   2.3.4-1.fc38               copr_base                                       155 k
 libmount                        s390x   2.38.1-3.fc38              fedora                                          132 k
 libnghttp2                      s390x   1.51.0-1.fc38              copr_base                                        78 k
 libnsl2                         s390x   2.0.0-4.fc38               copr_base                                        30 k
 libpkgconf                      s390x   1.8.0-3.fc37               fedora                                           34 k
 libpsl                          s390x   0.21.1-6.fc38              copr_base                                        66 k
 libpwquality                    s390x   1.4.5-1.fc38               fedora                                          119 k
 libselinux                      s390x   3.4-6.fc38                 copr_base                                        91 k
 libsemanage                     s390x   3.4-6.fc38                 copr_base                                       122 k
 libsepol                        s390x   3.4-4.fc38                 copr_base                                       330 k
 libsigsegv                      s390x   2.14-3.fc38                copr_base                                        27 k
 libsmartcols                    s390x   2.38.1-3.fc38              fedora                                           63 k
 libssh                          s390x   0.10.4-2.fc38              copr_base                                       206 k
 libssh-config                   noarch  0.10.4-2.fc38              copr_base                                       9.2 k
 libstdc++                       s390x   13.0.0-0.4.fc38            https_jakub_fedorapeople_org_fedora_gcc13_arch  889 k
 libtasn1                        s390x   4.19.0-1.fc38              copr_base                                        78 k
 libtirpc                        s390x   1.3.3-0.fc38               copr_base                                        97 k
 libunistring                    s390x   1.0-2.fc38                 copr_base                                       552 k
 libutempter                     s390x   1.2.1-7.fc38               copr_base                                        26 k
 libuuid                         s390x   2.38.1-3.fc38              fedora                                           27 k
 libverto                        s390x   0.3.2-4.fc38               copr_base                                        21 k
 libxcrypt                       s390x   4.4.33-5.fc38              copr_base                                       125 k
 libxml2                         s390x   2.10.3-2.fc38              copr_base                                       714 k
 libzstd                         s390x   1.5.2-3.fc37               fedora                                          274 k
 lua-libs                        s390x   5.4.4-6.fc38               copr_base                                       141 k
 lua-srpm-macros                 noarch  1-7.fc37                   fedora                                          8.8 k
 lz4-libs                        s390x   1.9.3-5.fc38               copr_base                                        88 k
 mpfr                            s390x   4.1.1-2.fc38               copr_base                                       553 k
 ncurses-base                    noarch  6.3-5.20221126.fc38        copr_base                                        62 k
 ncurses-libs                    s390x   6.3-5.20221126.fc38        copr_base                                       357 k
 nettle                          s390x   3.8-2.fc38                 copr_base                                       444 k
 nim-srpm-macros                 noarch  3-7.fc37                   fedora                                          8.4 k
 ocaml-srpm-macros               noarch  7-2.fc37                   fedora                                           13 k
 openblas-srpm-macros            noarch  2-12.fc37                  fedora                                          7.5 k
 openldap                        s390x   2.6.3-1.fc38               copr_base                                       262 k
 openssl-libs                    s390x   1:3.0.5-6.fc38             copr_base                                       1.8 M
 p11-kit                         s390x   0.24.1-5.fc38              copr_base                                       370 k
 p11-kit-trust                   s390x   0.24.1-5.fc38              copr_base                                       137 k
 package-notes-srpm-macros       noarch  0.5-6.fc38                 fedora                                           11 k
 pam                             s390x   1.5.2-15.fc38              copr_base                                       528 k
 pam-libs                        s390x   1.5.2-15.fc38              copr_base                                        59 k
 pcre2                           s390x   10.40-1.fc38.1             copr_base                                       251 k
 pcre2-syntax                    noarch  10.40-1.fc38.1             copr_base                                       143 k
 perl-srpm-macros                noarch  1-47.fc38                  fedora                                          8.2 k
 pkgconf                         s390x   1.8.0-3.fc37               fedora                                           41 k
 pkgconf-m4                      noarch  1.8.0-3.fc37               fedora                                           14 k
 pkgconf-pkg-config              s390x   1.8.0-3.fc37               fedora                                           10 k
 popt                            s390x   1.19-1.fc38                fedora                                           67 k
 publicsuffix-list-dafsa         noarch  20221208-1.fc38            fedora                                           59 k
 python-srpm-macros              noarch  3.11-6.fc38                fedora                                           25 k
 qt5-srpm-macros                 noarch  5.15.7-1.fc38              fedora                                          7.9 k
 readline                        s390x   8.2-2.fc38                 fedora                                          213 k
 rpm                             s390x   4.18.0-8.fc38              fedora                                          569 k
 rpm-build-libs                  s390x   4.18.0-8.fc38              fedora                                           92 k
 rpm-libs                        s390x   4.18.0-8.fc38              fedora                                          307 k
 rpm-sequoia                     s390x   1.2.0-1.fc38               fedora                                          960 k
 rpmautospec-rpm-macros          noarch  0.3.1-1.fc38               fedora                                          8.8 k
 rust-srpm-macros                noarch  23-1.fc38                  fedora                                          9.4 k
 setup                           noarch  2.14.3-1.fc38              fedora                                          152 k
 sqlite-libs                     s390x   3.40.0-1.fc38              fedora                                          651 k
 systemd-libs                    s390x   252.4-598.fc38             fedora                                          591 k
 tzdata                          noarch  2022g-1.fc38               fedora                                          716 k
 util-linux-core                 s390x   2.38.1-3.fc38              fedora                                          462 k
 xxhash-libs                     s390x   0.8.1-3.fc37               fedora                                           36 k
 xz-libs                         s390x   5.2.9-1.fc38               fedora                                           93 k
 zip                             s390x   3.0-35.fc38                fedora                                          261 k
 zlib                            s390x   1.2.13-1.fc38              fedora                                           96 k
 zstd                            s390x   1.5.2-3.fc37               fedora                                          410 k
Installing Groups:
 Buildsystem building group                                                                                              

Transaction Summary
=========================================================================================================================
Install  153 Packages

Total size: 52 M
Installed size: 182 M
Downloading Packages:
[SKIPPED] alternatives-1.21-1.fc38.s390x.rpm: Already downloaded               
[SKIPPED] authselect-1.4.2-1.fc38.s390x.rpm: Already downloaded                
[SKIPPED] authselect-libs-1.4.2-1.fc38.s390x.rpm: Already downloaded           
[SKIPPED] bash-5.2.9-3.fc38.s390x.rpm: Already downloaded                      
[SKIPPED] binutils-2.39-6.fc38.s390x.rpm: Already downloaded                   
[SKIPPED] binutils-gold-2.39-6.fc38.s390x.rpm: Already downloaded              
[SKIPPED] bzip2-1.0.8-12.fc38.s390x.rpm: Already downloaded                    
[SKIPPED] bzip2-libs-1.0.8-12.fc38.s390x.rpm: Already downloaded               
[SKIPPED] coreutils-9.1-8.fc38.s390x.rpm: Already downloaded                   
[SKIPPED] coreutils-common-9.1-8.fc38.s390x.rpm: Already downloaded            
[SKIPPED] cpio-2.13-13.fc38.s390x.rpm: Already downloaded                      
[SKIPPED] cracklib-2.9.7-30.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] curl-7.87.0-1.fc38.s390x.rpm: Already downloaded                     
[SKIPPED] cyrus-sasl-lib-2.1.28-8.fc38.s390x.rpm: Already downloaded           
[SKIPPED] diffutils-3.8-3.fc38.s390x.rpm: Already downloaded                   
[SKIPPED] dwz-0.15-1.fc38.s390x.rpm: Already downloaded                        
[SKIPPED] ed-1.18-2.fc38.s390x.rpm: Already downloaded                         
[SKIPPED] elfutils-0.188-3.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] elfutils-debuginfod-client-0.188-3.fc38.s390x.rpm: Already downloaded
[SKIPPED] elfutils-default-yama-scope-0.188-3.fc38.noarch.rpm: Already downloaded
[SKIPPED] elfutils-libelf-0.188-3.fc38.s390x.rpm: Already downloaded           
[SKIPPED] elfutils-libs-0.188-3.fc38.s390x.rpm: Already downloaded             
[SKIPPED] file-5.42-4.fc38.s390x.rpm: Already downloaded                       
[SKIPPED] file-libs-5.42-4.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] findutils-4.9.0-2.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] gawk-5.1.1-4.fc38.s390x.rpm: Already downloaded                      
[SKIPPED] gdbm-libs-1.23-2.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] gmp-6.2.1-3.fc38.s390x.rpm: Already downloaded                       
[SKIPPED] grep-3.8-1.fc38.s390x.rpm: Already downloaded                        
[SKIPPED] gzip-1.12-2.fc38.s390x.rpm: Already downloaded                       
[SKIPPED] jansson-2.13.1-5.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] keyutils-libs-1.6.1-5.fc38.s390x.rpm: Already downloaded             
[SKIPPED] krb5-libs-1.20.1-3.fc38.s390x.rpm: Already downloaded                
[SKIPPED] libacl-2.3.1-4.fc38.s390x.rpm: Already downloaded                    
[SKIPPED] libarchive-3.6.1-3.fc38.s390x.rpm: Already downloaded                
[SKIPPED] libattr-2.5.1-5.fc38.s390x.rpm: Already downloaded                   
[SKIPPED] libbrotli-1.0.9-9.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] libcap-2.48-5.fc38.s390x.rpm: Already downloaded                     
[SKIPPED] libcap-ng-0.8.3-4.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] libcom_err-1.46.5-3.fc38.s390x.rpm: Already downloaded               
[SKIPPED] libcurl-7.87.0-1.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] libdb-5.3.28-54.fc38.s390x.rpm: Already downloaded                   
[SKIPPED] libeconf-0.4.0-4.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] libevent-2.1.12-7.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] libffi-3.4.4-1.fc38.s390x.rpm: Already downloaded                    
[SKIPPED] libidn2-2.3.4-1.fc38.s390x.rpm: Already downloaded                   
[SKIPPED] libnghttp2-1.51.0-1.fc38.s390x.rpm: Already downloaded               
[SKIPPED] libnsl2-2.0.0-4.fc38.s390x.rpm: Already downloaded                   
[SKIPPED] libpsl-0.21.1-6.fc38.s390x.rpm: Already downloaded                   
[SKIPPED] libselinux-3.4-6.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] libsemanage-3.4-6.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] libsepol-3.4-4.fc38.s390x.rpm: Already downloaded                    
[SKIPPED] libsigsegv-2.14-3.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] libssh-0.10.4-2.fc38.s390x.rpm: Already downloaded                   
[SKIPPED] libssh-config-0.10.4-2.fc38.noarch.rpm: Already downloaded           
[SKIPPED] libtasn1-4.19.0-1.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] libtirpc-1.3.3-0.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] libunistring-1.0-2.fc38.s390x.rpm: Already downloaded                
[SKIPPED] libutempter-1.2.1-7.fc38.s390x.rpm: Already downloaded               
[SKIPPED] libverto-0.3.2-4.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] libxcrypt-4.4.33-5.fc38.s390x.rpm: Already downloaded                
[SKIPPED] libxml2-2.10.3-2.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] lua-libs-5.4.4-6.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] lz4-libs-1.9.3-5.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] mpfr-4.1.1-2.fc38.s390x.rpm: Already downloaded                      
[SKIPPED] ncurses-base-6.3-5.20221126.fc38.noarch.rpm: Already downloaded      
[SKIPPED] ncurses-libs-6.3-5.20221126.fc38.s390x.rpm: Already downloaded       
[SKIPPED] nettle-3.8-2.fc38.s390x.rpm: Already downloaded                      
[SKIPPED] openldap-2.6.3-1.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] openssl-libs-3.0.5-6.fc38.s390x.rpm: Already downloaded              
[SKIPPED] p11-kit-0.24.1-5.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] p11-kit-trust-0.24.1-5.fc38.s390x.rpm: Already downloaded            
[SKIPPED] pam-1.5.2-15.fc38.s390x.rpm: Already downloaded                      
[SKIPPED] pam-libs-1.5.2-15.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] patch-2.7.6-17.fc38.s390x.rpm: Already downloaded                    
[SKIPPED] pcre2-10.40-1.fc38.1.s390x.rpm: Already downloaded                   
[SKIPPED] pcre2-syntax-10.40-1.fc38.1.noarch.rpm: Already downloaded           
[SKIPPED] libgcc-13.0.0-0.4.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] libgomp-13.0.0-0.4.fc38.s390x.rpm: Already downloaded                
[SKIPPED] libstdc++-13.0.0-0.4.fc38.s390x.rpm: Already downloaded              
[SKIPPED] ansible-srpm-macros-1-8.1.fc38.noarch.rpm: Already downloaded        
[SKIPPED] audit-libs-3.0.9-2.fc38.s390x.rpm: Already downloaded                
[SKIPPED] basesystem-11-14.fc37.noarch.rpm: Already downloaded                 
[SKIPPED] ca-certificates-2022.2.54-5.fc37.noarch.rpm: Already downloaded      
[SKIPPED] crypto-policies-20221215-1.gita4c31a3.fc38.noarch.rpm: Already downloaded
[SKIPPED] debugedit-5.0-5.fc37.s390x.rpm: Already downloaded                   
[SKIPPED] efi-srpm-macros-5-6.fc37.noarch.rpm: Already downloaded              
[SKIPPED] fedora-gpg-keys-38-0.3.noarch.rpm: Already downloaded                
[SKIPPED] fedora-release-38-0.6.noarch.rpm: Already downloaded                 
[SKIPPED] fedora-release-common-38-0.6.noarch.rpm: Already downloaded          
[SKIPPED] fedora-release-identity-basic-38-0.6.noarch.rpm: Already downloaded  
[SKIPPED] fedora-repos-38-0.3.noarch.rpm: Already downloaded                   
[SKIPPED] fedora-repos-rawhide-38-0.3.noarch.rpm: Already downloaded           
[SKIPPED] filesystem-3.18-2.fc37.s390x.rpm: Already downloaded                 
[SKIPPED] fonts-srpm-macros-2.0.5-10.fc38.noarch.rpm: Already downloaded       
[SKIPPED] fpc-srpm-macros-1.3-6.fc37.noarch.rpm: Already downloaded            
[SKIPPED] gdb-minimal-12.1-10.fc38.s390x.rpm: Already downloaded               
[SKIPPED] ghc-srpm-macros-1.5.0-7.fc37.noarch.rpm: Already downloaded          
[SKIPPED] glibc-2.36.9000-19.fc38.s390x.rpm: Already downloaded                
[SKIPPED] glibc-common-2.36.9000-19.fc38.s390x.rpm: Already downloaded         
[SKIPPED] glibc-gconv-extra-2.36.9000-19.fc38.s390x.rpm: Already downloaded    
[SKIPPED] glibc-minimal-langpack-2.36.9000-19.fc38.s390x.rpm: Already downloaded
[SKIPPED] gnat-srpm-macros-4-16.fc37.noarch.rpm: Already downloaded            
[SKIPPED] go-srpm-macros-3.2.0-1.fc38.noarch.rpm: Already downloaded           
[SKIPPED] info-7.0.1-1.fc38.s390x.rpm: Already downloaded                      
[SKIPPED] kernel-srpm-macros-1.0-15.fc37.noarch.rpm: Already downloaded        
[SKIPPED] libblkid-2.38.1-3.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] libfdisk-2.38.1-3.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] libmount-2.38.1-3.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] libpkgconf-1.8.0-3.fc37.s390x.rpm: Already downloaded                
[SKIPPED] libpwquality-1.4.5-1.fc38.s390x.rpm: Already downloaded              
[SKIPPED] libsmartcols-2.38.1-3.fc38.s390x.rpm: Already downloaded             
[SKIPPED] libuuid-2.38.1-3.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] libzstd-1.5.2-3.fc37.s390x.rpm: Already downloaded                   
[SKIPPED] lua-srpm-macros-1-7.fc37.noarch.rpm: Already downloaded              
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[SKIPPED] publicsuffix-list-dafsa-20221208-1.fc38.noarch.rpm: Already downloaded
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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
fedora                                          1.6 MB/s | 1.6 kB     00:00    
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0x5323552A:
 Userid     : "Fedora (37) <fedora-37-primary@fedoraproject.org>"
 Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.18-2.fc37.s390x                           1/1 
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warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.14.3-1.fc38.noarch                          23/153 
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  Installing       : glibc-gconv-extra-2.36.9000-19.fc38.s390x           30/153 
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  Installing       : libsemanage-3.4-6.fc38.s390x                        77/153 
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  Installing       : nettle-3.8-2.fc38.s390x                             85/153 
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  Installing       : libxml2-2.10.3-2.fc38.s390x                         89/153 
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  Installing       : cpio-2.13-13.fc38.s390x                             93/153 
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  Installing       : cyrus-sasl-lib-2.1.28-8.fc38.s390x                  96/153 
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  Installing       : keyutils-libs-1.6.1-5.fc38.s390x                    98/153 
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  Installing       : libdb-5.3.28-54.fc38.s390x                         100/153 
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  Installing       : libnghttp2-1.51.0-1.fc38.s390x                     103/153 
  Installing       : libsigsegv-2.14-3.fc38.s390x                       104/153 
  Installing       : gawk-5.1.1-4.fc38.s390x                            105/153 
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  Installing       : pkgconf-1.8.0-3.fc37.s390x                         111/153 
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  Installing       : libssh-config-0.10.4-2.fc38.noarch                 114/153 
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  Installing       : coreutils-9.1-8.fc38.s390x                         117/153 
  Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch            118/153 
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  Installing       : cracklib-2.9.7-30.fc38.s390x                       123/153 
  Installing       : libpwquality-1.4.5-1.fc38.s390x                    124/153 
  Installing       : authselect-1.4.2-1.fc38.s390x                      125/153 
  Installing       : libnsl2-2.0.0-4.fc38.s390x                         126/153 
  Installing       : pam-1.5.2-15.fc38.s390x                            127/153 
  Installing       : libssh-0.10.4-2.fc38.s390x                         128/153 
  Installing       : libarchive-3.6.1-3.fc38.s390x                      129/153 
  Installing       : libevent-2.1.12-7.fc38.s390x                       130/153 
  Installing       : openldap-2.6.3-1.fc38.s390x                        131/153 
  Installing       : libcurl-7.87.0-1.fc38.s390x                        132/153 
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  Installing       : binutils-gold-2.39-6.fc38.s390x                    135/153 
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  Installing       : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch         145/153 
  Installing       : fonts-srpm-macros-1:2.0.5-10.fc38.noarch           146/153 
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  Verifying        : libcom_err-1.46.5-3.fc38.s390x                      40/153 
  Verifying        : libcurl-7.87.0-1.fc38.s390x                         41/153 
  Verifying        : libdb-5.3.28-54.fc38.s390x                          42/153 
  Verifying        : libeconf-0.4.0-4.fc38.s390x                         43/153 
  Verifying        : libevent-2.1.12-7.fc38.s390x                        44/153 
  Verifying        : libffi-3.4.4-1.fc38.s390x                           45/153 
  Verifying        : libidn2-2.3.4-1.fc38.s390x                          46/153 
  Verifying        : libnghttp2-1.51.0-1.fc38.s390x                      47/153 
  Verifying        : libnsl2-2.0.0-4.fc38.s390x                          48/153 
  Verifying        : libpsl-0.21.1-6.fc38.s390x                          49/153 
  Verifying        : libselinux-3.4-6.fc38.s390x                         50/153 
  Verifying        : libsemanage-3.4-6.fc38.s390x                        51/153 
  Verifying        : libsepol-3.4-4.fc38.s390x                           52/153 
  Verifying        : libsigsegv-2.14-3.fc38.s390x                        53/153 
  Verifying        : libssh-0.10.4-2.fc38.s390x                          54/153 
  Verifying        : libssh-config-0.10.4-2.fc38.noarch                  55/153 
  Verifying        : libtasn1-4.19.0-1.fc38.s390x                        56/153 
  Verifying        : libtirpc-1.3.3-0.fc38.s390x                         57/153 
  Verifying        : libunistring-1.0-2.fc38.s390x                       58/153 
  Verifying        : libutempter-1.2.1-7.fc38.s390x                      59/153 
  Verifying        : libverto-0.3.2-4.fc38.s390x                         60/153 
  Verifying        : libxcrypt-4.4.33-5.fc38.s390x                       61/153 
  Verifying        : libxml2-2.10.3-2.fc38.s390x                         62/153 
  Verifying        : lua-libs-5.4.4-6.fc38.s390x                         63/153 
  Verifying        : lz4-libs-1.9.3-5.fc38.s390x                         64/153 
  Verifying        : mpfr-4.1.1-2.fc38.s390x                             65/153 
  Verifying        : ncurses-base-6.3-5.20221126.fc38.noarch             66/153 
  Verifying        : ncurses-libs-6.3-5.20221126.fc38.s390x              67/153 
  Verifying        : nettle-3.8-2.fc38.s390x                             68/153 
  Verifying        : openldap-2.6.3-1.fc38.s390x                         69/153 
  Verifying        : openssl-libs-1:3.0.5-6.fc38.s390x                   70/153 
  Verifying        : p11-kit-0.24.1-5.fc38.s390x                         71/153 
  Verifying        : p11-kit-trust-0.24.1-5.fc38.s390x                   72/153 
  Verifying        : pam-1.5.2-15.fc38.s390x                             73/153 
  Verifying        : pam-libs-1.5.2-15.fc38.s390x                        74/153 
  Verifying        : patch-2.7.6-17.fc38.s390x                           75/153 
  Verifying        : pcre2-10.40-1.fc38.1.s390x                          76/153 
  Verifying        : pcre2-syntax-10.40-1.fc38.1.noarch                  77/153 
  Verifying        : libgcc-13.0.0-0.4.fc38.s390x                        78/153 
  Verifying        : libgomp-13.0.0-0.4.fc38.s390x                       79/153 
  Verifying        : libstdc++-13.0.0-0.4.fc38.s390x                     80/153 
  Verifying        : ansible-srpm-macros-1-8.1.fc38.noarch               81/153 
  Verifying        : audit-libs-3.0.9-2.fc38.s390x                       82/153 
  Verifying        : basesystem-11-14.fc37.noarch                        83/153 
  Verifying        : ca-certificates-2022.2.54-5.fc37.noarch             84/153 
  Verifying        : crypto-policies-20221215-1.gita4c31a3.fc38.noarc    85/153 
  Verifying        : debugedit-5.0-5.fc37.s390x                          86/153 
  Verifying        : efi-srpm-macros-5-6.fc37.noarch                     87/153 
  Verifying        : fedora-gpg-keys-38-0.3.noarch                       88/153 
  Verifying        : fedora-release-38-0.6.noarch                        89/153 
  Verifying        : fedora-release-common-38-0.6.noarch                 90/153 
  Verifying        : fedora-release-identity-basic-38-0.6.noarch         91/153 
  Verifying        : fedora-repos-38-0.3.noarch                          92/153 
  Verifying        : fedora-repos-rawhide-38-0.3.noarch                  93/153 
  Verifying        : filesystem-3.18-2.fc37.s390x                        94/153 
  Verifying        : fonts-srpm-macros-1:2.0.5-10.fc38.noarch            95/153 
  Verifying        : fpc-srpm-macros-1.3-6.fc37.noarch                   96/153 
  Verifying        : gdb-minimal-12.1-10.fc38.s390x                      97/153 
  Verifying        : ghc-srpm-macros-1.5.0-7.fc37.noarch                 98/153 
  Verifying        : glibc-2.36.9000-19.fc38.s390x                       99/153 
  Verifying        : glibc-common-2.36.9000-19.fc38.s390x               100/153 
  Verifying        : glibc-gconv-extra-2.36.9000-19.fc38.s390x          101/153 
  Verifying        : glibc-minimal-langpack-2.36.9000-19.fc38.s390x     102/153 
  Verifying        : gnat-srpm-macros-4-16.fc37.noarch                  103/153 
  Verifying        : go-srpm-macros-3.2.0-1.fc38.noarch                 104/153 
  Verifying        : info-7.0.1-1.fc38.s390x                            105/153 
  Verifying        : kernel-srpm-macros-1.0-15.fc37.noarch              106/153 
  Verifying        : libblkid-2.38.1-3.fc38.s390x                       107/153 
  Verifying        : libfdisk-2.38.1-3.fc38.s390x                       108/153 
  Verifying        : libmount-2.38.1-3.fc38.s390x                       109/153 
  Verifying        : libpkgconf-1.8.0-3.fc37.s390x                      110/153 
  Verifying        : libpwquality-1.4.5-1.fc38.s390x                    111/153 
  Verifying        : libsmartcols-2.38.1-3.fc38.s390x                   112/153 
  Verifying        : libuuid-2.38.1-3.fc38.s390x                        113/153 
  Verifying        : libzstd-1.5.2-3.fc37.s390x                         114/153 
  Verifying        : lua-srpm-macros-1-7.fc37.noarch                    115/153 
  Verifying        : nim-srpm-macros-3-7.fc37.noarch                    116/153 
  Verifying        : ocaml-srpm-macros-7-2.fc37.noarch                  117/153 
  Verifying        : openblas-srpm-macros-2-12.fc37.noarch              118/153 
  Verifying        : package-notes-srpm-macros-0.5-6.fc38.noarch        119/153 
  Verifying        : perl-srpm-macros-1-47.fc38.noarch                  120/153 
  Verifying        : pkgconf-1.8.0-3.fc37.s390x                         121/153 
  Verifying        : pkgconf-m4-1.8.0-3.fc37.noarch                     122/153 
  Verifying        : pkgconf-pkg-config-1.8.0-3.fc37.s390x              123/153 
  Verifying        : popt-1.19-1.fc38.s390x                             124/153 
  Verifying        : publicsuffix-list-dafsa-20221208-1.fc38.noarch     125/153 
  Verifying        : python-srpm-macros-3.11-6.fc38.noarch              126/153 
  Verifying        : qt5-srpm-macros-5.15.7-1.fc38.noarch               127/153 
  Verifying        : readline-8.2-2.fc38.s390x                          128/153 
  Verifying        : redhat-rpm-config-235-1.fc38.noarch                129/153 
  Verifying        : rpm-4.18.0-8.fc38.s390x                            130/153 
  Verifying        : rpm-build-4.18.0-8.fc38.s390x                      131/153 
  Verifying        : rpm-build-libs-4.18.0-8.fc38.s390x                 132/153 
  Verifying        : rpm-libs-4.18.0-8.fc38.s390x                       133/153 
  Verifying        : rpm-sequoia-1.2.0-1.fc38.s390x                     134/153 
  Verifying        : rpmautospec-rpm-macros-0.3.1-1.fc38.noarch         135/153 
  Verifying        : rust-srpm-macros-23-1.fc38.noarch                  136/153 
  Verifying        : sed-4.8-11.fc37.s390x                              137/153 
  Verifying        : setup-2.14.3-1.fc38.noarch                         138/153 
  Verifying        : shadow-utils-2:4.13-3.fc38.s390x                   139/153 
  Verifying        : sqlite-libs-3.40.0-1.fc38.s390x                    140/153 
  Verifying        : systemd-libs-252.4-598.fc38.s390x                  141/153 
  Verifying        : tar-2:1.34-5.fc38.s390x                            142/153 
  Verifying        : tzdata-2022g-1.fc38.noarch                         143/153 
  Verifying        : unzip-6.0-58.fc38.s390x                            144/153 
  Verifying        : util-linux-2.38.1-3.fc38.s390x                     145/153 
  Verifying        : util-linux-core-2.38.1-3.fc38.s390x                146/153 
  Verifying        : which-2.21-36.fc38.s390x                           147/153 
  Verifying        : xxhash-libs-0.8.1-3.fc37.s390x                     148/153 
  Verifying        : xz-5.2.9-1.fc38.s390x                              149/153 
  Verifying        : xz-libs-5.2.9-1.fc38.s390x                         150/153 
  Verifying        : zip-3.0-35.fc38.s390x                              151/153 
  Verifying        : zlib-1.2.13-1.fc38.s390x                           152/153 
  Verifying        : zstd-1.5.2-3.fc37.s390x                            153/153 

Installed:
  alternatives-1.21-1.fc38.s390x                                                
  ansible-srpm-macros-1-8.1.fc38.noarch                                         
  audit-libs-3.0.9-2.fc38.s390x                                                 
  authselect-1.4.2-1.fc38.s390x                                                 
  authselect-libs-1.4.2-1.fc38.s390x                                            
  basesystem-11-14.fc37.noarch                                                  
  bash-5.2.9-3.fc38.s390x                                                       
  binutils-2.39-6.fc38.s390x                                                    
  binutils-gold-2.39-6.fc38.s390x                                               
  bzip2-1.0.8-12.fc38.s390x                                                     
  bzip2-libs-1.0.8-12.fc38.s390x                                                
  ca-certificates-2022.2.54-5.fc37.noarch                                       
  coreutils-9.1-8.fc38.s390x                                                    
  coreutils-common-9.1-8.fc38.s390x                                             
  cpio-2.13-13.fc38.s390x                                                       
  cracklib-2.9.7-30.fc38.s390x                                                  
  crypto-policies-20221215-1.gita4c31a3.fc38.noarch                             
  curl-7.87.0-1.fc38.s390x                                                      
  cyrus-sasl-lib-2.1.28-8.fc38.s390x                                            
  debugedit-5.0-5.fc37.s390x                                                    
  diffutils-3.8-3.fc38.s390x                                                    
  dwz-0.15-1.fc38.s390x                                                         
  ed-1.18-2.fc38.s390x                                                          
  efi-srpm-macros-5-6.fc37.noarch                                               
  elfutils-0.188-3.fc38.s390x                                                   
  elfutils-debuginfod-client-0.188-3.fc38.s390x                                 
  elfutils-default-yama-scope-0.188-3.fc38.noarch                               
  elfutils-libelf-0.188-3.fc38.s390x                                            
  elfutils-libs-0.188-3.fc38.s390x                                              
  fedora-gpg-keys-38-0.3.noarch                                                 
  fedora-release-38-0.6.noarch                                                  
  fedora-release-common-38-0.6.noarch                                           
  fedora-release-identity-basic-38-0.6.noarch                                   
  fedora-repos-38-0.3.noarch                                                    
  fedora-repos-rawhide-38-0.3.noarch                                            
  file-5.42-4.fc38.s390x                                                        
  file-libs-5.42-4.fc38.s390x                                                   
  filesystem-3.18-2.fc37.s390x                                                  
  findutils-1:4.9.0-2.fc38.s390x                                                
  fonts-srpm-macros-1:2.0.5-10.fc38.noarch                                      
  fpc-srpm-macros-1.3-6.fc37.noarch                                             
  gawk-5.1.1-4.fc38.s390x                                                       
  gdb-minimal-12.1-10.fc38.s390x                                                
  gdbm-libs-1:1.23-2.fc38.s390x                                                 
  ghc-srpm-macros-1.5.0-7.fc37.noarch                                           
  glibc-2.36.9000-19.fc38.s390x                                                 
  glibc-common-2.36.9000-19.fc38.s390x                                          
  glibc-gconv-extra-2.36.9000-19.fc38.s390x                                     
  glibc-minimal-langpack-2.36.9000-19.fc38.s390x                                
  gmp-1:6.2.1-3.fc38.s390x                                                      
  gnat-srpm-macros-4-16.fc37.noarch                                             
  go-srpm-macros-3.2.0-1.fc38.noarch                                            
  grep-3.8-1.fc38.s390x                                                         
  gzip-1.12-2.fc38.s390x                                                        
  info-7.0.1-1.fc38.s390x                                                       
  jansson-2.13.1-5.fc38.s390x                                                   
  kernel-srpm-macros-1.0-15.fc37.noarch                                         
  keyutils-libs-1.6.1-5.fc38.s390x                                              
  krb5-libs-1.20.1-3.fc38.s390x                                                 
  libacl-2.3.1-4.fc38.s390x                                                     
  libarchive-3.6.1-3.fc38.s390x                                                 
  libattr-2.5.1-5.fc38.s390x                                                    
  libblkid-2.38.1-3.fc38.s390x                                                  
  libbrotli-1.0.9-9.fc38.s390x                                                  
  libcap-2.48-5.fc38.s390x                                                      
  libcap-ng-0.8.3-4.fc38.s390x                                                  
  libcom_err-1.46.5-3.fc38.s390x                                                
  libcurl-7.87.0-1.fc38.s390x                                                   
  libdb-5.3.28-54.fc38.s390x                                                    
  libeconf-0.4.0-4.fc38.s390x                                                   
  libevent-2.1.12-7.fc38.s390x                                                  
  libfdisk-2.38.1-3.fc38.s390x                                                  
  libffi-3.4.4-1.fc38.s390x                                                     
  libgcc-13.0.0-0.4.fc38.s390x                                                  
  libgomp-13.0.0-0.4.fc38.s390x                                                 
  libidn2-2.3.4-1.fc38.s390x                                                    
  libmount-2.38.1-3.fc38.s390x                                                  
  libnghttp2-1.51.0-1.fc38.s390x                                                
  libnsl2-2.0.0-4.fc38.s390x                                                    
  libpkgconf-1.8.0-3.fc37.s390x                                                 
  libpsl-0.21.1-6.fc38.s390x                                                    
  libpwquality-1.4.5-1.fc38.s390x                                               
  libselinux-3.4-6.fc38.s390x                                                   
  libsemanage-3.4-6.fc38.s390x                                                  
  libsepol-3.4-4.fc38.s390x                                                     
  libsigsegv-2.14-3.fc38.s390x                                                  
  libsmartcols-2.38.1-3.fc38.s390x                                              
  libssh-0.10.4-2.fc38.s390x                                                    
  libssh-config-0.10.4-2.fc38.noarch                                            
  libstdc++-13.0.0-0.4.fc38.s390x                                               
  libtasn1-4.19.0-1.fc38.s390x                                                  
  libtirpc-1.3.3-0.fc38.s390x                                                   
  libunistring-1.0-2.fc38.s390x                                                 
  libutempter-1.2.1-7.fc38.s390x                                                
  libuuid-2.38.1-3.fc38.s390x                                                   
  libverto-0.3.2-4.fc38.s390x                                                   
  libxcrypt-4.4.33-5.fc38.s390x                                                 
  libxml2-2.10.3-2.fc38.s390x                                                   
  libzstd-1.5.2-3.fc37.s390x                                                    
  lua-libs-5.4.4-6.fc38.s390x                                                   
  lua-srpm-macros-1-7.fc37.noarch                                               
  lz4-libs-1.9.3-5.fc38.s390x                                                   
  mpfr-4.1.1-2.fc38.s390x                                                       
  ncurses-base-6.3-5.20221126.fc38.noarch                                       
  ncurses-libs-6.3-5.20221126.fc38.s390x                                        
  nettle-3.8-2.fc38.s390x                                                       
  nim-srpm-macros-3-7.fc37.noarch                                               
  ocaml-srpm-macros-7-2.fc37.noarch                                             
  openblas-srpm-macros-2-12.fc37.noarch                                         
  openldap-2.6.3-1.fc38.s390x                                                   
  openssl-libs-1:3.0.5-6.fc38.s390x                                             
  p11-kit-0.24.1-5.fc38.s390x                                                   
  p11-kit-trust-0.24.1-5.fc38.s390x                                             
  package-notes-srpm-macros-0.5-6.fc38.noarch                                   
  pam-1.5.2-15.fc38.s390x                                                       
  pam-libs-1.5.2-15.fc38.s390x                                                  
  patch-2.7.6-17.fc38.s390x                                                     
  pcre2-10.40-1.fc38.1.s390x                                                    
  pcre2-syntax-10.40-1.fc38.1.noarch                                            
  perl-srpm-macros-1-47.fc38.noarch                                             
  pkgconf-1.8.0-3.fc37.s390x                                                    
  pkgconf-m4-1.8.0-3.fc37.noarch                                                
  pkgconf-pkg-config-1.8.0-3.fc37.s390x                                         
  popt-1.19-1.fc38.s390x                                                        
  publicsuffix-list-dafsa-20221208-1.fc38.noarch                                
  python-srpm-macros-3.11-6.fc38.noarch                                         
  qt5-srpm-macros-5.15.7-1.fc38.noarch                                          
  readline-8.2-2.fc38.s390x                                                     
  redhat-rpm-config-235-1.fc38.noarch                                           
  rpm-4.18.0-8.fc38.s390x                                                       
  rpm-build-4.18.0-8.fc38.s390x                                                 
  rpm-build-libs-4.18.0-8.fc38.s390x                                            
  rpm-libs-4.18.0-8.fc38.s390x                                                  
  rpm-sequoia-1.2.0-1.fc38.s390x                                                
  rpmautospec-rpm-macros-0.3.1-1.fc38.noarch                                    
  rust-srpm-macros-23-1.fc38.noarch                                             
  sed-4.8-11.fc37.s390x                                                         
  setup-2.14.3-1.fc38.noarch                                                    
  shadow-utils-2:4.13-3.fc38.s390x                                              
  sqlite-libs-3.40.0-1.fc38.s390x                                               
  systemd-libs-252.4-598.fc38.s390x                                             
  tar-2:1.34-5.fc38.s390x                                                       
  tzdata-2022g-1.fc38.noarch                                                    
  unzip-6.0-58.fc38.s390x                                                       
  util-linux-2.38.1-3.fc38.s390x                                                
  util-linux-core-2.38.1-3.fc38.s390x                                           
  which-2.21-36.fc38.s390x                                                      
  xxhash-libs-0.8.1-3.fc37.s390x                                                
  xz-5.2.9-1.fc38.s390x                                                         
  xz-libs-5.2.9-1.fc38.s390x                                                    
  zip-3.0-35.fc38.s390x                                                         
  zlib-1.2.13-1.fc38.s390x                                                      
  zstd-1.5.2-3.fc37.s390x                                                       

Complete!
Finish: dnf install
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: libattr-2.5.1-5.fc38.s390x
xz-5.2.9-1.fc38.s390x
ghc-srpm-macros-1.5.0-7.fc37.noarch
libgomp-13.0.0-0.4.fc38.s390x
libtirpc-1.3.3-0.fc38.s390x
libxcrypt-4.4.33-5.fc38.s390x
pam-libs-1.5.2-15.fc38.s390x
libblkid-2.38.1-3.fc38.s390x
libcurl-7.87.0-1.fc38.s390x
popt-1.19-1.fc38.s390x
gnat-srpm-macros-4-16.fc37.noarch
libverto-0.3.2-4.fc38.s390x
p11-kit-trust-0.24.1-5.fc38.s390x
libssh-0.10.4-2.fc38.s390x
libdb-5.3.28-54.fc38.s390x
coreutils-9.1-8.fc38.s390x
rpm-sequoia-1.2.0-1.fc38.s390x
libnsl2-2.0.0-4.fc38.s390x
libselinux-3.4-6.fc38.s390x
rust-srpm-macros-23-1.fc38.noarch
nim-srpm-macros-3-7.fc37.noarch
libxml2-2.10.3-2.fc38.s390x
libnghttp2-1.51.0-1.fc38.s390x
libpwquality-1.4.5-1.fc38.s390x
info-7.0.1-1.fc38.s390x
libmount-2.38.1-3.fc38.s390x
gmp-6.2.1-3.fc38.s390x
audit-libs-3.0.9-2.fc38.s390x
cpio-2.13-13.fc38.s390x
libevent-2.1.12-7.fc38.s390x
gdb-minimal-12.1-10.fc38.s390x
shadow-utils-4.13-3.fc38.s390x
diffutils-3.8-3.fc38.s390x
libuuid-2.38.1-3.fc38.s390x
redhat-rpm-config-235-1.fc38.noarch
rpmautospec-rpm-macros-0.3.1-1.fc38.noarch
util-linux-2.38.1-3.fc38.s390x
rpm-build-libs-4.18.0-8.fc38.s390x
zlib-1.2.13-1.fc38.s390x
gdbm-libs-1.23-2.fc38.s390x
lua-libs-5.4.4-6.fc38.s390x
p11-kit-0.24.1-5.fc38.s390x
libffi-3.4.4-1.fc38.s390x
lua-srpm-macros-1-7.fc37.noarch
pkgconf-m4-1.8.0-3.fc37.noarch
fedora-gpg-keys-38-0.3.noarch
elfutils-debuginfod-client-0.188-3.fc38.s390x
fedora-release-identity-basic-38-0.6.noarch
systemd-libs-252.4-598.fc38.s390x
sed-4.8-11.fc37.s390x
bzip2-libs-1.0.8-12.fc38.s390x
pkgconf-pkg-config-1.8.0-3.fc37.s390x
ocaml-srpm-macros-7-2.fc37.noarch
libsemanage-3.4-6.fc38.s390x
libpsl-0.21.1-6.fc38.s390x
zstd-1.5.2-3.fc37.s390x
efi-srpm-macros-5-6.fc37.noarch
elfutils-libs-0.188-3.fc38.s390x
basesystem-11-14.fc37.noarch
ed-1.18-2.fc38.s390x
findutils-4.9.0-2.fc38.s390x
openldap-2.6.3-1.fc38.s390x
bzip2-1.0.8-12.fc38.s390x
openssl-libs-3.0.5-6.fc38.s390x
file-libs-5.42-4.fc38.s390x
fedora-release-common-38-0.6.noarch
go-srpm-macros-3.2.0-1.fc38.noarch
glibc-2.36.9000-19.fc38.s390x
ansible-srpm-macros-1-8.1.fc38.noarch
libbrotli-1.0.9-9.fc38.s390x
patch-2.7.6-17.fc38.s390x
authselect-libs-1.4.2-1.fc38.s390x
xz-libs-5.2.9-1.fc38.s390x
libutempter-1.2.1-7.fc38.s390x
tar-1.34-5.fc38.s390x
fedora-repos-rawhide-38-0.3.noarch
pkgconf-1.8.0-3.fc37.s390x
libacl-2.3.1-4.fc38.s390x
nettle-3.8-2.fc38.s390x
lz4-libs-1.9.3-5.fc38.s390x
debugedit-5.0-5.fc37.s390x
package-notes-srpm-macros-0.5-6.fc38.noarch
ncurses-libs-6.3-5.20221126.fc38.s390x
xxhash-libs-0.8.1-3.fc37.s390x
krb5-libs-1.20.1-3.fc38.s390x
libeconf-0.4.0-4.fc38.s390x
libcap-2.48-5.fc38.s390x
readline-8.2-2.fc38.s390x
coreutils-common-9.1-8.fc38.s390x
libgcc-13.0.0-0.4.fc38.s390x
which-2.21-36.fc38.s390x
unzip-6.0-58.fc38.s390x
perl-srpm-macros-1-47.fc38.noarch
libzstd-1.5.2-3.fc37.s390x
fedora-repos-38-0.3.noarch
glibc-common-2.36.9000-19.fc38.s390x
bash-5.2.9-3.fc38.s390x
pcre2-syntax-10.40-1.fc38.1.noarch
alternatives-1.21-1.fc38.s390x
cracklib-2.9.7-30.fc38.s390x
curl-7.87.0-1.fc38.s390x
qt5-srpm-macros-5.15.7-1.fc38.noarch
rpm-build-4.18.0-8.fc38.s390x
sqlite-libs-3.40.0-1.fc38.s390x
dwz-0.15-1.fc38.s390x
openblas-srpm-macros-2-12.fc37.noarch
jansson-2.13.1-5.fc38.s390x
glibc-gconv-extra-2.36.9000-19.fc38.s390x
glibc-minimal-langpack-2.36.9000-19.fc38.s390x
libcom_err-1.46.5-3.fc38.s390x
tzdata-2022g-1.fc38.noarch
libsepol-3.4-4.fc38.s390x
cyrus-sasl-lib-2.1.28-8.fc38.s390x
filesystem-3.18-2.fc37.s390x
binutils-gold-2.39-6.fc38.s390x
libstdc++-13.0.0-0.4.fc38.s390x
kernel-srpm-macros-1.0-15.fc37.noarch
elfutils-default-yama-scope-0.188-3.fc38.noarch
ncurses-base-6.3-5.20221126.fc38.noarch
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
gawk-5.1.1-4.fc38.s390x
elfutils-0.188-3.fc38.s390x
elfutils-libelf-0.188-3.fc38.s390x
setup-2.14.3-1.fc38.noarch
util-linux-core-2.38.1-3.fc38.s390x
gpg-pubkey-5323552a-6112bcdc
keyutils-libs-1.6.1-5.fc38.s390x
libsigsegv-2.14-3.fc38.s390x
authselect-1.4.2-1.fc38.s390x
libsmartcols-2.38.1-3.fc38.s390x
grep-3.8-1.fc38.s390x
gpg-pubkey-eb10b464-6202d9c6
file-5.42-4.fc38.s390x
pcre2-10.40-1.fc38.1.s390x
ca-certificates-2022.2.54-5.fc37.noarch
gzip-1.12-2.fc38.s390x
publicsuffix-list-dafsa-20221208-1.fc38.noarch
libfdisk-2.38.1-3.fc38.s390x
libcap-ng-0.8.3-4.fc38.s390x
libtasn1-4.19.0-1.fc38.s390x
libpkgconf-1.8.0-3.fc37.s390x
fonts-srpm-macros-2.0.5-10.fc38.noarch
rpm-4.18.0-8.fc38.s390x
mpfr-4.1.1-2.fc38.s390x
zip-3.0-35.fc38.s390x
libssh-config-0.10.4-2.fc38.noarch
libidn2-2.3.4-1.fc38.s390x
libunistring-1.0-2.fc38.s390x
libarchive-3.6.1-3.fc38.s390x
binutils-2.39-6.fc38.s390x
python-srpm-macros-3.11-6.fc38.noarch
pam-1.5.2-15.fc38.s390x
fpc-srpm-macros-1.3-6.fc37.noarch
rpm-libs-4.18.0-8.fc38.s390x
fedora-release-38-0.6.noarch
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1658448000
Wrote: /builddir/build/SRPMS/percolator-3.05-10.fc38.src.rpm
Finish: rpmbuild -bs
cp: ‘var/lib/mock/fedora-rawhide-s390x-1672058577.895426/root/var/log’: No such file or directory
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-s390x-1672058577.895426/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-s390x-1672058577.895426/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-s390x-1672058577.895426/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-jo428f29/percolator/percolator.spec) Config(child) 1 minutes 44 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=115200): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/percolator-3.05-10.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1672058577.895426 -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/percolator-3.05-10.fc38.src.rpm)  Config(fedora-rawhide-s390x)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1672058577.895426/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1672058577.895426/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1672058577.895426/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                                 4.4 kB/s | 3.0 kB     00:00    
Additional repo https_jakub_fedorapeople_org_fe 4.2 kB/s | 3.0 kB     00:00    
fedora                                          2.6 kB/s | 6.6 kB     00:02    
Dependencies resolved.
Nothing to do.
Complete!
Finish: dnf update
Finish: chroot init
Start: build phase for percolator-3.05-10.fc38.src.rpm
Start: build setup for percolator-3.05-10.fc38.src.rpm
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1658448000
Wrote: /builddir/build/SRPMS/percolator-3.05-10.fc38.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                 542  B/s | 3.0 kB     00:05    
Copr repository                                 4.3 MB/s |  29 MB     00:06    
Additional repo https_jakub_fedorapeople_org_fe 4.2 kB/s | 3.0 kB     00:00    
fedora                                           11 kB/s | 6.6 kB     00:00    
Dependencies resolved.
==============================================================================================================
 Package                     Arch    Version             Repository                                       Size
==============================================================================================================
Installing:
 boost-devel                 s390x   1.78.0-9.fc38       copr_base                                        11 M
 boost-static                s390x   1.78.0-9.fc38       copr_base                                       3.8 M
 bzip2-devel                 s390x   1.0.8-12.fc38       copr_base                                       214 k
 cmake                       s390x   3.25.1-1.fc38       copr_base                                       6.9 M
 gcc                         s390x   13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch   28 M
 gcc-c++                     s390x   13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch   11 M
 libtirpc-devel              s390x   1.3.3-0.fc38        copr_base                                       113 k
 make                        s390x   1:4.3-11.fc38       copr_base                                       550 k
 sqlite-devel                s390x   3.40.0-1.fc38       fedora                                          143 k
 tokyocabinet-devel          s390x   1.4.48-20.fc37      fedora                                           93 k
 xerces-c-devel              s390x   3.2.3-7.fc37        fedora                                          509 k
 xsd                         s390x   4.1.0-0.10.a11.fc37 fedora                                          1.2 M
 zlib-devel                  s390x   1.2.13-1.fc38       fedora                                           45 k
Installing dependencies:
 annobin-docs                noarch  10.99-1.0.1.fc38    https_jakub_fedorapeople_org_fedora_gcc13_arch   93 k
 annobin-plugin-gcc          s390x   10.99-1.0.1.fc38    https_jakub_fedorapeople_org_fedora_gcc13_arch  888 k
 boost                       s390x   1.78.0-9.fc38       copr_base                                        15 k
 boost-atomic                s390x   1.78.0-9.fc38       copr_base                                        20 k
 boost-chrono                s390x   1.78.0-9.fc38       copr_base                                        27 k
 boost-container             s390x   1.78.0-9.fc38       copr_base                                        42 k
 boost-context               s390x   1.78.0-9.fc38       copr_base                                        18 k
 boost-contract              s390x   1.78.0-9.fc38       copr_base                                        47 k
 boost-coroutine             s390x   1.78.0-9.fc38       copr_base                                        23 k
 boost-date-time             s390x   1.78.0-9.fc38       copr_base                                        16 k
 boost-fiber                 s390x   1.78.0-9.fc38       copr_base                                        44 k
 boost-filesystem            s390x   1.78.0-9.fc38       copr_base                                        67 k
 boost-graph                 s390x   1.78.0-9.fc38       copr_base                                       161 k
 boost-iostreams             s390x   1.78.0-9.fc38       copr_base                                        41 k
 boost-json                  s390x   1.78.0-9.fc38       copr_base                                       116 k
 boost-locale                s390x   1.78.0-9.fc38       copr_base                                       228 k
 boost-log                   s390x   1.78.0-9.fc38       copr_base                                       501 k
 boost-math                  s390x   1.78.0-9.fc38       copr_base                                       225 k
 boost-nowide                s390x   1.78.0-9.fc38       copr_base                                        22 k
 boost-numpy3                s390x   1.78.0-9.fc38       copr_base                                        30 k
 boost-program-options       s390x   1.78.0-9.fc38       copr_base                                       111 k
 boost-python3               s390x   1.78.0-9.fc38       copr_base                                        96 k
 boost-random                s390x   1.78.0-9.fc38       copr_base                                        26 k
 boost-regex                 s390x   1.78.0-9.fc38       copr_base                                       124 k
 boost-serialization         s390x   1.78.0-9.fc38       copr_base                                       136 k
 boost-stacktrace            s390x   1.78.0-9.fc38       copr_base                                        31 k
 boost-system                s390x   1.78.0-9.fc38       copr_base                                        16 k
 boost-test                  s390x   1.78.0-9.fc38       copr_base                                       252 k
 boost-thread                s390x   1.78.0-9.fc38       copr_base                                        61 k
 boost-timer                 s390x   1.78.0-9.fc38       copr_base                                        26 k
 boost-type_erasure          s390x   1.78.0-9.fc38       copr_base                                        35 k
 boost-wave                  s390x   1.78.0-9.fc38       copr_base                                       246 k
 cmake-data                  noarch  3.25.1-1.fc38       copr_base                                       1.7 M
 cmake-filesystem            s390x   3.25.1-1.fc38       copr_base                                        17 k
 cmake-rpm-macros            noarch  3.25.1-1.fc38       copr_base                                        16 k
 cpp                         s390x   13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch  8.9 M
 emacs-filesystem            noarch  1:28.1-3.fc37       fedora                                          9.5 k
 expat                       s390x   2.5.0-1.fc38        copr_base                                       114 k
 flexiblas                   s390x   3.2.1-3.fc38        fedora                                           32 k
 flexiblas-netlib            s390x   3.2.1-3.fc38        fedora                                          2.9 M
 flexiblas-openblas-openmp   s390x   3.2.1-3.fc38        fedora                                           17 k
 gc                          s390x   8.2.2-1.fc38        copr_base                                       114 k
 gcc-plugin-annobin          s390x   13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch   28 k
 glibc-devel                 s390x   2.36.9000-19.fc38   fedora                                           55 k
 glibc-headers-s390          noarch  2.36.9000-19.fc38   fedora                                          516 k
 guile22                     s390x   2.2.7-6.fc38        copr_base                                       6.4 M
 jsoncpp                     s390x   1.9.5-3.fc38        copr_base                                        97 k
 kernel-headers              s390x   6.1.0-1.fc38        fedora                                          1.5 M
 libasan                     s390x   13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch  492 k
 libatomic                   s390x   13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch   18 k
 libb2                       s390x   0.98.1-7.fc38       copr_base                                        27 k
 libcutl                     s390x   1.10.0-25.fc38      copr_base                                       328 k
 libgfortran                 s390x   13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch  560 k
 libicu                      s390x   71.1-2.fc38         copr_base                                        10 M
 libicu-devel                s390x   71.1-2.fc38         copr_base                                       842 k
 libmpc                      s390x   1.2.1-5.fc38        copr_base                                        65 k
 libstdc++-devel             s390x   13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch  2.4 M
 libtool-ltdl                s390x   2.4.7-3.0.1.fc38    https_jakub_fedorapeople_org_fedora_gcc13_arch   38 k
 libubsan                    s390x   13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch  203 k
 libuv                       s390x   1:1.44.2-2.fc38     copr_base                                       154 k
 libxcrypt-devel             s390x   4.4.33-5.fc38       copr_base                                        31 k
 mpdecimal                   s390x   2.5.1-4.fc38        copr_base                                       115 k
 openblas                    s390x   0.3.21-4.fc38       copr_base                                        35 k
 openblas-openmp             s390x   0.3.21-4.fc38       copr_base                                       4.3 M
 python-pip-wheel            noarch  22.3.1-1.fc38       fedora                                          1.4 M
 python-setuptools-wheel     noarch  65.5.1-1.fc38       fedora                                          715 k
 python3                     s390x   3.11.1-1.fc38       fedora                                           27 k
 python3-libs                s390x   3.11.1-1.fc38       fedora                                          9.5 M
 python3-numpy               s390x   1:1.23.5-1.fc38     copr_base                                       7.1 M
 rhash                       s390x   1.4.3-1.fc38        fedora                                          193 k
 sqlite                      s390x   3.40.0-1.fc38       fedora                                          791 k
 tokyocabinet                s390x   1.4.48-20.fc37      fedora                                          499 k
 vim-filesystem              noarch  2:9.0.1054-1.fc38   fedora                                           19 k
 xerces-c                    s390x   3.2.3-7.fc37        fedora                                          877 k

Transaction Summary
==============================================================================================================
Install  87 Packages

Total size: 131 M
Total download size: 49 M
Installed size: 594 M
Downloading Packages:
[SKIPPED] bzip2-devel-1.0.8-12.fc38.s390x.rpm: Already downloaded              
[SKIPPED] cmake-3.25.1-1.fc38.s390x.rpm: Already downloaded                    
[SKIPPED] cmake-data-3.25.1-1.fc38.noarch.rpm: Already downloaded              
[SKIPPED] cmake-filesystem-3.25.1-1.fc38.s390x.rpm: Already downloaded         
[SKIPPED] cmake-rpm-macros-3.25.1-1.fc38.noarch.rpm: Already downloaded        
[SKIPPED] expat-2.5.0-1.fc38.s390x.rpm: Already downloaded                     
[SKIPPED] gc-8.2.2-1.fc38.s390x.rpm: Already downloaded                        
[SKIPPED] guile22-2.2.7-6.fc38.s390x.rpm: Already downloaded                   
[SKIPPED] jsoncpp-1.9.5-3.fc38.s390x.rpm: Already downloaded                   
[SKIPPED] libb2-0.98.1-7.fc38.s390x.rpm: Already downloaded                    
[SKIPPED] libicu-71.1-2.fc38.s390x.rpm: Already downloaded                     
[SKIPPED] libicu-devel-71.1-2.fc38.s390x.rpm: Already downloaded               
[SKIPPED] libmpc-1.2.1-5.fc38.s390x.rpm: Already downloaded                    
[SKIPPED] libuv-1.44.2-2.fc38.s390x.rpm: Already downloaded                    
[SKIPPED] libxcrypt-devel-4.4.33-5.fc38.s390x.rpm: Already downloaded          
[SKIPPED] make-4.3-11.fc38.s390x.rpm: Already downloaded                       
[SKIPPED] mpdecimal-2.5.1-4.fc38.s390x.rpm: Already downloaded                 
[SKIPPED] annobin-docs-10.99-1.0.1.fc38.noarch.rpm: Already downloaded         
[SKIPPED] annobin-plugin-gcc-10.99-1.0.1.fc38.s390x.rpm: Already downloaded    
[SKIPPED] cpp-13.0.0-0.4.fc38.s390x.rpm: Already downloaded                    
[SKIPPED] gcc-13.0.0-0.4.fc38.s390x.rpm: Already downloaded                    
[SKIPPED] gcc-plugin-annobin-13.0.0-0.4.fc38.s390x.rpm: Already downloaded     
[SKIPPED] libasan-13.0.0-0.4.fc38.s390x.rpm: Already downloaded                
[SKIPPED] libatomic-13.0.0-0.4.fc38.s390x.rpm: Already downloaded              
[SKIPPED] libtool-ltdl-2.4.7-3.0.1.fc38.s390x.rpm: Already downloaded          
[SKIPPED] libubsan-13.0.0-0.4.fc38.s390x.rpm: Already downloaded               
[SKIPPED] emacs-filesystem-28.1-3.fc37.noarch.rpm: Already downloaded          
[SKIPPED] glibc-devel-2.36.9000-19.fc38.s390x.rpm: Already downloaded          
[SKIPPED] glibc-headers-s390-2.36.9000-19.fc38.noarch.rpm: Already downloaded  
[SKIPPED] kernel-headers-6.1.0-1.fc38.s390x.rpm: Already downloaded            
[SKIPPED] python-pip-wheel-22.3.1-1.fc38.noarch.rpm: Already downloaded        
[SKIPPED] python-setuptools-wheel-65.5.1-1.fc38.noarch.rpm: Already downloaded 
[SKIPPED] python3-3.11.1-1.fc38.s390x.rpm: Already downloaded                  
[SKIPPED] python3-libs-3.11.1-1.fc38.s390x.rpm: Already downloaded             
[SKIPPED] rhash-1.4.3-1.fc38.s390x.rpm: Already downloaded                     
[SKIPPED] sqlite-3.40.0-1.fc38.s390x.rpm: Already downloaded                   
[SKIPPED] sqlite-devel-3.40.0-1.fc38.s390x.rpm: Already downloaded             
[SKIPPED] vim-filesystem-9.0.1054-1.fc38.noarch.rpm: Already downloaded        
[SKIPPED] zlib-devel-1.2.13-1.fc38.s390x.rpm: Already downloaded               
(40/87): boost-chrono-1.78.0-9.fc38.s390x.rpm    70 kB/s |  27 kB     00:00    
(41/87): boost-1.78.0-9.fc38.s390x.rpm           38 kB/s |  15 kB     00:00    
(42/87): boost-atomic-1.78.0-9.fc38.s390x.rpm    51 kB/s |  20 kB     00:00    
(43/87): boost-contract-1.78.0-9.fc38.s390x.rpm 6.0 MB/s |  47 kB     00:00    
(44/87): boost-container-1.78.0-9.fc38.s390x.rp 4.0 MB/s |  42 kB     00:00    
(45/87): boost-context-1.78.0-9.fc38.s390x.rpm  1.6 MB/s |  18 kB     00:00    
(46/87): boost-coroutine-1.78.0-9.fc38.s390x.rp 2.8 MB/s |  23 kB     00:00    
(47/87): boost-date-time-1.78.0-9.fc38.s390x.rp 1.0 MB/s |  16 kB     00:00    
(48/87): boost-fiber-1.78.0-9.fc38.s390x.rpm    4.0 MB/s |  44 kB     00:00    
(49/87): boost-graph-1.78.0-9.fc38.s390x.rpm    6.2 MB/s | 161 kB     00:00    
(50/87): boost-iostreams-1.78.0-9.fc38.s390x.rp 7.2 MB/s |  41 kB     00:00    
(51/87): boost-filesystem-1.78.0-9.fc38.s390x.r 1.6 MB/s |  67 kB     00:00    
(52/87): boost-json-1.78.0-9.fc38.s390x.rpm      12 MB/s | 116 kB     00:00    
(53/87): boost-locale-1.78.0-9.fc38.s390x.rpm    14 MB/s | 228 kB     00:00    
(54/87): boost-log-1.78.0-9.fc38.s390x.rpm       25 MB/s | 501 kB     00:00    
(55/87): boost-math-1.78.0-9.fc38.s390x.rpm      17 MB/s | 225 kB     00:00    
(56/87): boost-nowide-1.78.0-9.fc38.s390x.rpm   1.5 MB/s |  22 kB     00:00    
(57/87): boost-numpy3-1.78.0-9.fc38.s390x.rpm   5.6 MB/s |  30 kB     00:00    
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(78/87): gcc-c++-13.0.0-0.4.fc38.s390x.rpm      2.1 MB/s |  11 MB     00:05    
(79/87): libstdc++-devel-13.0.0-0.4.fc38.s390x. 455 kB/s | 2.4 MB     00:05    
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(81/87): flexiblas-openblas-openmp-3.2.1-3.fc38  34 kB/s |  17 kB     00:00    
(82/87): tokyocabinet-devel-1.4.48-20.fc37.s390 186 kB/s |  93 kB     00:00    
(83/87): tokyocabinet-1.4.48-20.fc37.s390x.rpm  669 kB/s | 499 kB     00:00    
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(85/87): xerces-c-devel-3.2.3-7.fc37.s390x.rpm  2.9 MB/s | 509 kB     00:00    
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(87/87): xerces-c-3.2.3-7.fc37.s390x.rpm        1.2 MB/s | 877 kB     00:00    
--------------------------------------------------------------------------------
Total                                           3.6 MB/s |  49 MB     00:13     
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Transaction check succeeded.
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Installed:
  annobin-docs-10.99-1.0.1.fc38.noarch                                          
  annobin-plugin-gcc-10.99-1.0.1.fc38.s390x                                     
  boost-1.78.0-9.fc38.s390x                                                     
  boost-atomic-1.78.0-9.fc38.s390x                                              
  boost-chrono-1.78.0-9.fc38.s390x                                              
  boost-container-1.78.0-9.fc38.s390x                                           
  boost-context-1.78.0-9.fc38.s390x                                             
  boost-contract-1.78.0-9.fc38.s390x                                            
  boost-coroutine-1.78.0-9.fc38.s390x                                           
  boost-date-time-1.78.0-9.fc38.s390x                                           
  boost-devel-1.78.0-9.fc38.s390x                                               
  boost-fiber-1.78.0-9.fc38.s390x                                               
  boost-filesystem-1.78.0-9.fc38.s390x                                          
  boost-graph-1.78.0-9.fc38.s390x                                               
  boost-iostreams-1.78.0-9.fc38.s390x                                           
  boost-json-1.78.0-9.fc38.s390x                                                
  boost-locale-1.78.0-9.fc38.s390x                                              
  boost-log-1.78.0-9.fc38.s390x                                                 
  boost-math-1.78.0-9.fc38.s390x                                                
  boost-nowide-1.78.0-9.fc38.s390x                                              
  boost-numpy3-1.78.0-9.fc38.s390x                                              
  boost-program-options-1.78.0-9.fc38.s390x                                     
  boost-python3-1.78.0-9.fc38.s390x                                             
  boost-random-1.78.0-9.fc38.s390x                                              
  boost-regex-1.78.0-9.fc38.s390x                                               
  boost-serialization-1.78.0-9.fc38.s390x                                       
  boost-stacktrace-1.78.0-9.fc38.s390x                                          
  boost-static-1.78.0-9.fc38.s390x                                              
  boost-system-1.78.0-9.fc38.s390x                                              
  boost-test-1.78.0-9.fc38.s390x                                                
  boost-thread-1.78.0-9.fc38.s390x                                              
  boost-timer-1.78.0-9.fc38.s390x                                               
  boost-type_erasure-1.78.0-9.fc38.s390x                                        
  boost-wave-1.78.0-9.fc38.s390x                                                
  bzip2-devel-1.0.8-12.fc38.s390x                                               
  cmake-3.25.1-1.fc38.s390x                                                     
  cmake-data-3.25.1-1.fc38.noarch                                               
  cmake-filesystem-3.25.1-1.fc38.s390x                                          
  cmake-rpm-macros-3.25.1-1.fc38.noarch                                         
  cpp-13.0.0-0.4.fc38.s390x                                                     
  emacs-filesystem-1:28.1-3.fc37.noarch                                         
  expat-2.5.0-1.fc38.s390x                                                      
  flexiblas-3.2.1-3.fc38.s390x                                                  
  flexiblas-netlib-3.2.1-3.fc38.s390x                                           
  flexiblas-openblas-openmp-3.2.1-3.fc38.s390x                                  
  gc-8.2.2-1.fc38.s390x                                                         
  gcc-13.0.0-0.4.fc38.s390x                                                     
  gcc-c++-13.0.0-0.4.fc38.s390x                                                 
  gcc-plugin-annobin-13.0.0-0.4.fc38.s390x                                      
  glibc-devel-2.36.9000-19.fc38.s390x                                           
  glibc-headers-s390-2.36.9000-19.fc38.noarch                                   
  guile22-2.2.7-6.fc38.s390x                                                    
  jsoncpp-1.9.5-3.fc38.s390x                                                    
  kernel-headers-6.1.0-1.fc38.s390x                                             
  libasan-13.0.0-0.4.fc38.s390x                                                 
  libatomic-13.0.0-0.4.fc38.s390x                                               
  libb2-0.98.1-7.fc38.s390x                                                     
  libcutl-1.10.0-25.fc38.s390x                                                  
  libgfortran-13.0.0-0.4.fc38.s390x                                             
  libicu-71.1-2.fc38.s390x                                                      
  libicu-devel-71.1-2.fc38.s390x                                                
  libmpc-1.2.1-5.fc38.s390x                                                     
  libstdc++-devel-13.0.0-0.4.fc38.s390x                                         
  libtirpc-devel-1.3.3-0.fc38.s390x                                             
  libtool-ltdl-2.4.7-3.0.1.fc38.s390x                                           
  libubsan-13.0.0-0.4.fc38.s390x                                                
  libuv-1:1.44.2-2.fc38.s390x                                                   
  libxcrypt-devel-4.4.33-5.fc38.s390x                                           
  make-1:4.3-11.fc38.s390x                                                      
  mpdecimal-2.5.1-4.fc38.s390x                                                  
  openblas-0.3.21-4.fc38.s390x                                                  
  openblas-openmp-0.3.21-4.fc38.s390x                                           
  python-pip-wheel-22.3.1-1.fc38.noarch                                         
  python-setuptools-wheel-65.5.1-1.fc38.noarch                                  
  python3-3.11.1-1.fc38.s390x                                                   
  python3-libs-3.11.1-1.fc38.s390x                                              
  python3-numpy-1:1.23.5-1.fc38.s390x                                           
  rhash-1.4.3-1.fc38.s390x                                                      
  sqlite-3.40.0-1.fc38.s390x                                                    
  sqlite-devel-3.40.0-1.fc38.s390x                                              
  tokyocabinet-1.4.48-20.fc37.s390x                                             
  tokyocabinet-devel-1.4.48-20.fc37.s390x                                       
  vim-filesystem-2:9.0.1054-1.fc38.noarch                                       
  xerces-c-3.2.3-7.fc37.s390x                                                   
  xerces-c-devel-3.2.3-7.fc37.s390x                                             
  xsd-4.1.0-0.10.a11.fc37.s390x                                                 
  zlib-devel-1.2.13-1.fc38.s390x                                                

Complete!
Finish: build setup for percolator-3.05-10.fc38.src.rpm
Start: rpmbuild percolator-3.05-10.fc38.src.rpm
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1658448000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.j05tQQ
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf percolator-rel-3-05
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/percolator-rel-3-05.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd percolator-rel-3-05
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ tar -xvf /builddir/build/SOURCES/yeast-01.sqt.tar.gz
yeast-01.shuffled2.sqt
yeast-01.shuffled.sqt
yeast-01.sqt
+ find . -type f -name '*.cpp' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.h' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.xx' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.txt' -exec chmod 0644 '{}' ';'
+ chmod a-x src/converters/MSToolkit/RAMP/README
+ mv src/converters/MSToolkit/RAMP/README src/converters/MSToolkit/RAMP/RAMP-README
+ mv src/converters/MSToolkit/RAMP/Readme.Mike.txt src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt
+ cp -p /builddir/build/SOURCES/percolator-RAMP_license_lgpl-2.1.txt RAMP_license_lgpl-2.1.txt
+ sed -e 's|./bin|bin|g' -i src/qvality/CMakeLists.txt
+ sed -e 's|${ELUDE_MODELS_PATH}..|${ELUDE_MODELS_PATH}|g' -i src/elude_tool/CMakeLists.txt
+ sed -e 's|${CMAKE_INSTALL_PREFIX}/share/elude/models/|${CMAKE_INSTALL_PREFIX}/share/elude|g' -i src/elude_tool/CMakeLists.txt
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.osH79o
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -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 percolator-rel-3-05
+ export 'CXXFLAGS=-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ mkdir -p percolator
~/build/BUILD/percolator-rel-3-05/percolator ~/build/BUILD/percolator-rel-3-05
+ pushd percolator
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -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
+ /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DXML_SUPPORT:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -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 -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=s390x ..
-- The C compiler identification is GNU 13.0.0
-- The CXX compiler identification is GNU 13.0.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- CMAKE_PREFIX_PATH = ../
-- XML_SUPPORT = ON
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = s390x
-- TOOL CHAIN FILE = 
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages:
-- Found Xerces-C: /usr/lib64/libxerces-c.so
--               : /usr/include
--        Version: 3.2.3
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Locating CodeSynthesis library with XSDDIR set to 
-- Package CodeSynthesis XSD found: /usr/include, /usr/bin/xsdcxx
-- Found Boost: /usr/lib64/cmake/Boost-1.78.0/BoostConfig.cmake (found suitable version "1.78.0", minimum required is "1.46.0")  
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_SKIP_INSTALL_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR


-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-05/percolator
+ cd src
+ xsdcxx cxx-tree --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../../src/xml/percolator_in.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../../src/xml/percolator_out.xsd
+ cd ..
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05 -B/builddir/build/BUILD/percolator-rel-3-05/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/percolator//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
/usr/bin/make  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend
/usr/bin/make  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src /builddir/build/BUILD/percolator-rel-3-05/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake --color=
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/usr/bin/make  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake --color=
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[  2%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o -MF CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o -MF CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp
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[  8%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o -MF CMakeFiles/picked_protein.dir/Database.cpp.o.d -o CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Database.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Database.cpp: In member function 'void PercolatorCrux::Database::print(FILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Database.cpp:206:12: warning: unused variable 'protein' [-Wunused-variable]
  206 |   Protein* protein = NULL;
      |            ^~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Peptide.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Peptide.cpp:375:13: warning: 'bool equal_peptides(char*, PercolatorCrux::Peptide*)' defined but not used [-Wunused-function]
  375 | static bool equal_peptides(
      |             ^~~~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PeptideConstraint.cpp
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PeptideSrc.cpp
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o -MF CMakeFiles/perclibrary.dir/percolator_in.cxx.o.d -o CMakeFiles/perclibrary.dir/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/percolator/src/percolator_in.cxx
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PickedProteinCaller.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PickedProteinCaller.cpp: In member function 'bool PickedProteinCaller::getProteinFragmentsAndDuplicates(std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/PickedProteinCaller.cpp:365:8: warning: unused variable 'success' [-Wunused-variable]
  365 |   bool success = true;
      |        ^~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o -MF CMakeFiles/picked_protein.dir/Protein.cpp.o.d -o CMakeFiles/picked_protein.dir/Protein.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp: In member function 'void PercolatorCrux::Protein::shuffle(PercolatorCrux::DECOY_TYPE_T)':
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:529:9: warning: enumeration value 'PEPTIDE_REVERSE_DECOYS' not handled in switch [-Wswitch]
  529 |   switch(decoy_type){
      |         ^
In function 'PercolatorCrux::Protein::readRawSequence(_IO_FILE*, char*, unsigned int, char*, unsigned int*)',
    inlined from 'PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)' at /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:505:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  505 |   raw_sequence[i_seq] = '\0';
      |   ~~~~~~~~~~~~~~~~~~~~^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp: In member function 'PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:355:15: note: at offset 40000 into destination object 'PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)::buffer' of size 40000
  355 |   static char buffer[PROTEIN_SEQUENCE_LENGTH];///> The sequence to read in.
      |               ^~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/daxpy.c.o -MF CMakeFiles/blas.dir/daxpy.c.o.d -o CMakeFiles/blas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-rel-3-05/src/blas/daxpy.c
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/ddot.c.o -MF CMakeFiles/blas.dir/ddot.c.o.d -o CMakeFiles/blas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-rel-3-05/src/blas/ddot.c
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dgemv.c.o -MF CMakeFiles/blas.dir/dgemv.c.o.d -o CMakeFiles/blas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-rel-3-05/src/blas/dgemv.c
/builddir/build/BUILD/percolator-rel-3-05/src/blas/dgemv.c: In function 'dgemv_':
/builddir/build/BUILD/percolator-rel-3-05/src/blas/dgemv.c:59:45: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
   59 |     if (*m == 0 || *n == 0 || *alpha == 0.0 && *beta == 1.0) {
      |                               ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dnrm2.c.o -MF CMakeFiles/blas.dir/dnrm2.c.o.d -o CMakeFiles/blas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-rel-3-05/src/blas/dnrm2.c
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dscal.c.o -MF CMakeFiles/blas.dir/dscal.c.o.d -o CMakeFiles/blas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-rel-3-05/src/blas/dscal.c
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/cmake -P CMakeFiles/blas.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas && /usr/bin/cmake -E cmake_link_script CMakeFiles/blas.dir/link.txt --verbose=1
/usr/bin/ar rcv libblas.a CMakeFiles/blas.dir/daxpy.c.o CMakeFiles/blas.dir/ddot.c.o CMakeFiles/blas.dir/dgemv.c.o CMakeFiles/blas.dir/dnrm2.c.o CMakeFiles/blas.dir/dscal.c.o
a - CMakeFiles/blas.dir/daxpy.c.o
a - CMakeFiles/blas.dir/ddot.c.o
a - CMakeFiles/blas.dir/dgemv.c.o
a - CMakeFiles/blas.dir/dnrm2.c.o
a - CMakeFiles/blas.dir/dscal.c.o
/usr/bin/ranlib libblas.a
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/fido /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 28%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o -MF CMakeFiles/fido.dir/BasicBigraph.cpp.o.d -o CMakeFiles/fido.dir/BasicBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/StringTable.h:9,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:6:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
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[ 14%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o -MF CMakeFiles/perclibrary.dir/percolator_out.cxx.o.d -o CMakeFiles/perclibrary.dir/percolator_out.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/percolator/src/percolator_out.cxx
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/parser.cxx.o -MF CMakeFiles/perclibrary.dir/parser.cxx.o.d -o CMakeFiles/perclibrary.dir/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In constructor 'parser_impl::parser_impl()':
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:106:33: warning: 'parser_impl::gp_' will be initialized after [-Wreorder]
  106 |   std::auto_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
      |                                 ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:102:22: warning:   'xercesc_3_2::DOMImplementation& parser_impl::dom_impl_' [-Wreorder]
  102 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
  144 | parser_impl::parser_impl() : clean_(true),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In member function 'xsd::cxx::xml::dom::auto_ptr<xercesc_3_2::DOMDocument> parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable]
  178 |       size_t n(s.size());
      |              ^
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:170:9: warning: unused variable 'i' [-Wunused-variable]
  170 |     int i(1);
      |         ^
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/serializer.cxx.o -MF CMakeFiles/perclibrary.dir/serializer.cxx.o.d -o CMakeFiles/perclibrary.dir/serializer.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/src/serializer.cxx
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 33%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -MF CMakeFiles/perclibrary.dir/BaseSpline.cpp.o.d -o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 29%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o -MF CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o.d -o CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 34%] Building CXX object src/CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o -MF CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o.d -o CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/DescriptionOfCorrect.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DescriptionOfCorrect.cpp:23:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:39:6: warning: 'void Array<T>::add(const T&) [with T = int]' was hidden [-Woverloaded-virtual=]
   39 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:14:8: note:   by 'void Set::add(int)'
   14 |   void add(int el);
      |        ^~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 37%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o -MF CMakeFiles/perclibrary.dir/MassHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/MassHandler.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 38%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescription.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescription.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 40%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o -MF CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o.d -o CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:21:
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC()':
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:26:1: warning:   when initialized here [-Wreorder]
   26 | PSMDescriptionDOC::PSMDescriptionDOC() :
      | ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC(std::string, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:30:1: warning:   when initialized here [-Wreorder]
   30 | PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) :
      | ^~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 41%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ResultHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ResultHolder.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 36%] Building CXX object src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o -MF CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o.d -o CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 44%] Building CXX object src/fido/CMakeFiles/fido.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/Numerical.cpp.o -MF CMakeFiles/fido.dir/Numerical.cpp.o.d -o CMakeFiles/fido.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 42%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -MF CMakeFiles/perclibrary.dir/XMLInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h:29,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h: In constructor 'XMLInterface::XMLInterface(const std::string&, bool, bool, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h:99:8: warning: 'XMLInterface::reportUniquePeptides_' will be initialized after [-Wreorder]
   99 |   bool reportUniquePeptides_;
      |        ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.h:93:8: warning:   'bool XMLInterface::printDecoys_' [-Wreorder]
   93 |   bool printDecoys_, printExpMass_;
      |        ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp:58:1: warning:   when initialized here [-Wreorder]
   58 | XMLInterface::XMLInterface(const std::string& outputFN,
      | ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp: In member function 'int XMLInterface::readAndScorePin(std::istream&, std::vector<double>&, Scores&, const std::string&, SetHandler&, SanityCheck*&, ProteinProbEstimator*, Enzyme*&)':
/builddir/build/BUILD/percolator-rel-3-05/src/XMLInterface.cpp:257:26: warning: unused variable 'numFeatures' [-Wunused-variable]
  257 |       const unsigned int numFeatures = FeatureNames::getNumFeatures();
      |                          ^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 45%] Building CXX object src/fido/CMakeFiles/fido.dir/Random.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/Random.cpp.o -MF CMakeFiles/fido.dir/Random.cpp.o.d -o CMakeFiles/fido.dir/Random.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Random.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 48%] Building CXX object src/fido/CMakeFiles/fido.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/Set.cpp.o -MF CMakeFiles/fido.dir/Set.cpp.o.d -o CMakeFiles/fido.dir/Set.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 49%] Building CXX object src/fido/CMakeFiles/fido.dir/Vector.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/fido/CMakeFiles/fido.dir/Vector.cpp.o -MF CMakeFiles/fido.dir/Vector.cpp.o.d -o CMakeFiles/fido.dir/Vector.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 50%] Linking CXX static library libfido.a
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido && /usr/bin/cmake -E cmake_link_script CMakeFiles/fido.dir/link.txt --verbose=1
/usr/bin/ar qc libfido.a CMakeFiles/fido.dir/BasicBigraph.cpp.o CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o CMakeFiles/fido.dir/Numerical.cpp.o CMakeFiles/fido.dir/Random.cpp.o CMakeFiles/fido.dir/Set.cpp.o CMakeFiles/fido.dir/Vector.cpp.o
/usr/bin/ranlib libfido.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 50%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o -MF CMakeFiles/perclibrary.dir/SetHandler.cpp.o.d -o CMakeFiles/perclibrary.dir/SetHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp: In member function 'int SetHandler::getNumFeatures(const std::string&, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:158:10: warning: variable 'a' set but not used [-Wunused-but-set-variable]
  158 |   double a = reader.readDouble();
      |          ^
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp: In member function 'void SetHandler::readPSMs(std::istream&, std::string&, bool, bool&, std::vector<OptionalField>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:290:18: warning: unused variable 'targetIdx' [-Wunused-variable]
  290 |     unsigned int targetIdx = 0u, decoyIdx = 0u;
      |                  ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:290:34: warning: unused variable 'decoyIdx' [-Wunused-variable]
  290 |     unsigned int targetIdx = 0u, decoyIdx = 0u;
      |                                  ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp: In member function 'int SetHandler::readAndScoreTab(std::istream&, std::vector<double>&, Scores&, SanityCheck*&)':
/builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.cpp:489:46: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  489 |   if (hasDefaultValues && init_values.size() > numFeatures) {
      |                           ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/StdvNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/svm.cpp.o -MF CMakeFiles/perclibrary.dir/svm.cpp.o.d -o CMakeFiles/perclibrary.dir/svm.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/svm.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -MF CMakeFiles/perclibrary.dir/CrossValidation.cpp.o.d -o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:28,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:29:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h: In constructor 'CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, int, bool, int, bool, unsigned int, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:101:8: warning: 'CrossValidation::trainBestPositive_' will be initialized after [-Wreorder]
  101 |   bool trainBestPositive_;
      |        ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.h:90:16: warning:   'unsigned int CrossValidation::numThreads_' [-Wreorder]
   90 |   unsigned int numThreads_;
      |                ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:32:1: warning:   when initialized here [-Wreorder]
   32 | CrossValidation::CrossValidation(bool quickValidation,
      | ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'int CrossValidation::preIterationSetup(Scores&, SanityCheck*, Normalizer*, FeatureMemoryPool&)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:106:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  106 |   for (int set = 0; set < numFolds_; ++set) {
      |                     ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:107:39: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  107 |     for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) {
      |                             ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:141:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  141 |     for (int set = 0; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:145:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  145 |     for (int set = 0; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'int CrossValidation::doStep(bool, Normalizer*, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:263:25: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  263 |   for (int set = 0; set < numFolds_; ++set) {
      |                     ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:269:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  269 |     for (int set = 0; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:291:26: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  291 |    for (int set = 0; set < numFolds_; ++set) {
      |                      ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:303:42: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  303 |      for (int nestedFold = 0; nestedFold < nestedXvalBins_; ++nestedFold)
      |                               ~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:318:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<candidateCposCfrac>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  318 |    for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++){
      |                          ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'void CrossValidation::trainCpCnPair(candidateCposCfrac&, options*, AlgIn*)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:343:16: warning: unused variable 'set' [-Wunused-variable]
  343 |   unsigned int set = cpCnFold.set;
      |                ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:344:16: warning: unused variable 'nestedFold' [-Wunused-variable]
  344 |   unsigned int nestedFold = cpCnFold.nestedSet;
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:356:7: warning: unused variable 'tp' [-Wunused-variable]
  356 |   int tp = 0;
      |       ^~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'int CrossValidation::mergeCpCnPairs(double, options*, std::vector<std::vector<Scores> >&, const std::vector<double>&, const std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:399:21: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  399 |   for (set = 0; set < numFolds_; ++set) {
      |                 ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:439:23: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  439 |     for (set = 0; set < numFolds_; ++set) {
      |                   ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:474:21: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  474 |   for (set = 0; set < numFolds_; ++set) {
      |                 ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp: In member function 'void CrossValidation::postIterationProcessing(Scores&, SanityCheck*)':
/builddir/build/BUILD/percolator-rel-3-05/src/CrossValidation.cpp:483:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  483 |     for (int set = 0; set < numFolds_; ++set) {
      |                       ~~~~^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 57%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Enzyme.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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[ 58%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Globals.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Normalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.h: In constructor 'SanityCheck::SanityCheck()':
/builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.h:87:8: warning: 'SanityCheck::concatenatedSearch_' will be initialized after [-Wreorder]
   87 |   bool concatenatedSearch_;
      |        ^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.h:72:10: warning:   'double SanityCheck::test_fdr_' [-Wreorder]
   72 |   double test_fdr_, initial_train_fdr_;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/SanityCheck.cpp:31:1: warning:   when initialized here [-Wreorder]
   31 | SanityCheck::SanityCheck() :
      | ^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 62%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/UniNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 64%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/DataSet.cpp.o -MF CMakeFiles/perclibrary.dir/DataSet.cpp.o.d -o CMakeFiles/perclibrary.dir/DataSet.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp: In member function 'void DataSet::print_features()':
/builddir/build/BUILD/percolator-rel-3-05/src/DataSet.cpp:69:21: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   69 |   for (int i = 0; i < getSize(); i++) {
      |                   ~~^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 54%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Caller.cpp.o -MF CMakeFiles/perclibrary.dir/Caller.cpp.o.d -o CMakeFiles/perclibrary.dir/Caller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.h: In constructor 'Caller::Caller()':
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:103:48: warning: 'Caller::trainBestPositive_' will be initialized after [-Wreorder]
  103 |   bool reportEachIteration_, quickValidation_, trainBestPositive_,
      |                                                ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:101:59: warning:   'unsigned int Caller::numThreads_' [-Wreorder]
  101 |   unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_;
      |                                                           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp:35:1: warning:   when initialized here [-Wreorder]
   35 | Caller::Caller() :
      | ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp: In member function 'bool Caller::parseOptions(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/Caller.cpp:694:7: warning: label 'std' defined but not used [-Wunused-label]
  694 |       std:cerr << "Error: the --static option requires the --init-weights "
      |       ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureNames.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/FeatureNames.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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[ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -MF CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o.d -o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Option.cpp.o -MF CMakeFiles/perclibrary.dir/Option.cpp.o.d -o CMakeFiles/perclibrary.dir/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 70%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h: In constructor 'ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:238:16: warning: 'ProteinProbEstimator::absenceRatio_' will be initialized after [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |                ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:238:10: warning:   'double ProteinProbEstimator::pi0_' [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:242:16: warning: 'ProteinProbEstimator::numberTargetProteins_' will be initialized after [-Wreorder]
  242 |   unsigned int numberTargetProteins_;
      |                ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:237:8: warning:   'bool ProteinProbEstimator::usePi0_' [-Wreorder]
  237 |   bool usePi0_;
      |        ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:243:15: warning: 'ProteinProbEstimator::decoyPattern_' will be initialized after [-Wreorder]
  243 |   std::string decoyPattern_;
      |               ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:240:10: warning:   'double ProteinProbEstimator::fdr_' [-Wreorder]
  240 |   double fdr_;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -MF CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o.d -o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.cpp:37:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.cpp: In static member function 'static void PosteriorEstimator::getQValuesFromPEP(const std::vector<double>&, std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.cpp:468:21: warning: unused variable 'queue' [-Wunused-variable]
  468 |         int nP = 1, queue = 0;
      |                     ^~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ProteinFDRestimator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 74%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -MF CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o.d -o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PseudoRandom.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/SqtSanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ssl.cpp.o -MF CMakeFiles/perclibrary.dir/ssl.cpp.o.d -o CMakeFiles/perclibrary.dir/ssl.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'void cglsFun2(int, int*, const double*, double*, int, int, double*, double*, double*, double*, double, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:86:7: warning: unused variable 'ind' [-Wunused-variable]
   86 |   int ind = 0;
      |       ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:87:10: warning: unused variable 'temp' [-Wunused-variable]
   87 |   double temp = 0.0;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'int CGLS(const AlgIn&, double, int, double, const vector_int*, vector_double*, vector_double*, double, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:117:19: warning: unused variable 'j' [-Wunused-variable]
  117 |   register int i, j;
      |                   ^
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'int L2_SVM_MFN(const AlgIn&, options*, vector_double*, vector_double*, double, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:251:10: warning: unused variable 't' [-Wunused-variable]
  251 |   double t = 0.0;
      |          ^
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp: In function 'double line_search(double*, double*, double, double*, double*, const double*, int, int, double, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:364:7: warning: unused variable 'inc' [-Wunused-variable]
  364 |   int inc = 1;
      |       ^~~
In function 'Clear(options*)',
    inlined from 'Clear(options*)' at /builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:440:6:
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:442:12: warning: pointer 'opt_2(D)' used after 'operator delete[](void*)' [-Wuse-after-free]
  442 |   delete[] opt;
      |            ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/ssl.cpp:441:12: note: call to 'operator delete[](void*)' here
  441 |   delete[] opt;
      |            ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 78%] Building CXX object src/CMakeFiles/perclibrary.dir/EludeModel.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/EludeModel.cpp.o -MF CMakeFiles/perclibrary.dir/EludeModel.cpp.o.d -o CMakeFiles/perclibrary.dir/EludeModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/EludeModel.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/EludeModel.cpp:34:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o -MF CMakeFiles/perclibrary.dir/PackedVector.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedVector.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.cpp:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -MF CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o.d -o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PackedMatrix.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedMatrix.h:11,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedMatrix.cpp:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 82%] Building CXX object src/CMakeFiles/perclibrary.dir/Matrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Matrix.cpp.o -MF CMakeFiles/perclibrary.dir/Matrix.cpp.o.d -o CMakeFiles/perclibrary.dir/Matrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Matrix.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/Matrix.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/Matrix.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 84%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Logger.cpp.o -MF CMakeFiles/perclibrary.dir/Logger.cpp.o.d -o CMakeFiles/perclibrary.dir/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Logger.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 85%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/MyException.cpp.o -MF CMakeFiles/perclibrary.dir/MyException.cpp.o.d -o CMakeFiles/perclibrary.dir/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/MyException.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/Scores.cpp.o -MF CMakeFiles/perclibrary.dir/Scores.cpp.o.d -o CMakeFiles/perclibrary.dir/Scores.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp:32:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp: In member function 'void Scores::populateWithPSMs(SetHandler&)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp:292:29: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  292 |   if (totalNumberOfTargets_ <= (unsigned)(FeatureNames::getNumFeatures() * 5)) {
      |       ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.cpp:295:28: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  295 |   if (totalNumberOfDecoys_ <= (unsigned)(FeatureNames::getNumFeatures() * 5)) {
      |       ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 88%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -MF CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o.d -o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.h: In constructor 'ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.h:108:8: warning: 'ProteinScoreHolder::isDecoy_' will be initialized after [-Wreorder]
  108 |   bool isDecoy_;
      |        ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.h:106:7: warning:   'int ProteinScoreHolder::groupId_' [-Wreorder]
  106 |   int groupId_;
      |       ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/ProteinScoreHolder.cpp:20:1: warning:   when initialized here [-Wreorder]
   20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide,
      | ^~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 86%] Building CXX object src/CMakeFiles/perclibrary.dir/FidoInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/FidoInterface.cpp.o -MF CMakeFiles/perclibrary.dir/FidoInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/FidoInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h:20,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h: In constructor 'FidoInterface::FidoInterface(double, double, double, bool, bool, bool, unsigned int, double, double, double, double, bool, std::string, bool, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h:110:10: warning: 'FidoInterface::mseThreshold_' will be initialized after [-Wreorder]
  110 |   double mseThreshold_;
      |          ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.h:106:8: warning:   'bool FidoInterface::doGridSearch_' [-Wreorder]
  106 |   bool doGridSearch_;
      |        ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:76:1: warning:   when initialized here [-Wreorder]
   76 | FidoInterface::FidoInterface(double alpha, double beta, double gamma,
      | ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp: In member function 'double FidoInterface::estimatePriors(Scores&)':
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:132:10: warning: variable 'prior' set but not used [-Wunused-but-set-variable]
  132 |   double prior, prior2, prior3, prior4;
      |          ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp: In member function 'void FidoInterface::getEstimated_and_Empirical_FDR(const std::vector<std::vector<std::__cxx11::basic_string<char> > >&, const std::vector<double>&, std::vector<double>&, std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:556:12: warning: unused variable 'prob' [-Wunused-variable]
  556 |     double prob = probabilities[k];
      |            ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/FidoInterface.cpp:558:14: warning: unused variable 'fpChange' [-Wunused-variable]
  558 |     unsigned fpChange = proteinNames[k].size() - tpChange;
      |              ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 90%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -MF CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o.d -o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/FeatureMemoryPool.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 89%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -MF CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o.d -o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:27,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h: In constructor 'PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:86:10: warning: 'PickedProteinInterface::maxPeptidePval_' will be initialized after [-Wreorder]
   86 |   double maxPeptidePval_;
      |          ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:85:8: warning:   'bool PickedProteinInterface::reportFragmentProteins_' [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |        ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:85:33: warning: 'PickedProteinInterface::reportDuplicateProteins_' will be initialized after [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.h:83:26: warning:   'ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_' [-Wreorder]
   83 |   ProteinInferenceMethod protInferenceMethod_;
      |                          ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp: In member function 'virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*)':
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:165:36: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  165 |     if (total_non_enzymatic_flanks > peptideScores.size()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp: In member function 'virtual void PickedProteinInterface::computeProbabilities(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/PickedProteinInterface.cpp:344:13: warning: unused variable 'significantPeptides' [-Wunused-variable]
  344 |         int significantPeptides = 0;
      |             ^~~~~~~~~~~~~~~~~~~
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[ 92%] Linking CXX static library libperclibrary.a
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary.dir/link.txt --verbose=1
/usr/bin/ar qc libperclibrary.a CMakeFiles/perclibrary.dir/percolator_in.cxx.o CMakeFiles/perclibrary.dir/percolator_out.cxx.o CMakeFiles/perclibrary.dir/parser.cxx.o CMakeFiles/perclibrary.dir/serializer.cxx.o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o CMakeFiles/perclibrary.dir/DescriptionOfCorrect.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/PSMDescriptionDOC.cpp.o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o CMakeFiles/perclibrary.dir/SetHandler.cpp.o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o CMakeFiles/perclibrary.dir/svm.cpp.o CMakeFiles/perclibrary.dir/Caller.cpp.o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o CMakeFiles/perclibrary.dir/Enzyme.cpp.o CMakeFiles/perclibrary.dir/Globals.cpp.o CMakeFiles/perclibrary.dir/Normalizer.cpp.o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o CMakeFiles/perclibrary.dir/DataSet.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Option.cpp.o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o CMakeFiles/perclibrary.dir/ssl.cpp.o CMakeFiles/perclibrary.dir/EludeModel.cpp.o CMakeFiles/perclibrary.dir/PackedVector.cpp.o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o CMakeFiles/perclibrary.dir/Matrix.cpp.o CMakeFiles/perclibrary.dir/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/FidoInterface.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
/usr/bin/ranlib libperclibrary.a
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src /builddir/build/BUILD/percolator-rel-3-05/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake --color=
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake --color=
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[ 97%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o -MF CMakeFiles/qvality.dir/qvality_main.cpp.o.d -o CMakeFiles/qvality.dir/qvality_main.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/qvality/qvality_main.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/./PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/./BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/./LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/./PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/qvality/qvality_main.cpp:20:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 96%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-05/percolator/src -I/builddir/build/BUILD/percolator-rel-3-05/src/. -I/builddir/build/BUILD/percolator-rel-3-05/src/fido -I/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/CMakeFiles/percolator.dir/main.cpp.o -MF CMakeFiles/percolator.dir/main.cpp.o.d -o CMakeFiles/percolator.dir/main.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/main.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:31,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/Caller.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/main.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 98%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality && /usr/bin/cmake -E cmake_link_script CMakeFiles/qvality.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -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 -Wl,-z,relro   -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 -ltirpc -rdynamic CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality   -L/builddir/build/BUILD/percolator-rel-3-05/percolator/src  ../libperclibrary.a ../fido/libfido.a 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[100%] Built target qvality
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[100%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-rel-3-05/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -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 -Wl,-z,relro   -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 -ltirpc -rdynamic CMakeFiles/percolator.dir/main.cpp.o -o percolator  libperclibrary.a blas/libblas.a fido/libfido.a picked_protein/libpicked_protein.a -lxerces-c -lstdc++ 
In function 'readRawSequence',
    inlined from 'parseProteinFastaFile' at /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:505:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  505 |   raw_sequence[i_seq] = '\0';
      |                       ^
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp: In member function 'parseProteinFastaFile':
/builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/Protein.cpp:355:15: note: at offset 40000 into destination object 'buffer' of size 40000
  355 |   static char buffer[PROTEIN_SEQUENCE_LENGTH];///> The sequence to read in.
      |               ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[100%] Built target percolator
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-05
+ mkdir -p fido
+ pushd fido
~/build/BUILD/percolator-rel-3-05/fido ~/build/BUILD/percolator-rel-3-05
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -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
+ /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_BUILD_TYPE:STRING=Release -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -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 -ltirpc' -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=s390x ../src/fido
-- The C compiler identification is GNU 13.0.0
-- The CXX compiler identification is GNU 13.0.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_C_FLAGS_RELEASE
    CMAKE_EXE_LINKER_FLAGS_RELEASE
    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_SKIP_INSTALL_RPATH
    CMAKE_SKIP_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR
    TARGET_ARCH
    TokyoCabinet_INCLUDE_DIR
    TokyoCabinet_LIBRARY


-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-05/fido
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/fido -B/builddir/build/BUILD/percolator-rel-3-05/fido --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/fido/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/fido//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
/usr/bin/make  -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
cd /builddir/build/BUILD/percolator-rel-3-05/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/fido /builddir/build/BUILD/percolator-rel-3-05/src/fido /builddir/build/BUILD/percolator-rel-3-05/fido /builddir/build/BUILD/percolator-rel-3-05/fido /builddir/build/BUILD/percolator-rel-3-05/fido/CMakeFiles/fido.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
/usr/bin/make  -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 25%] Building CXX object CMakeFiles/fido.dir/BasicGroupBigraph.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/BasicGroupBigraph.o -MF CMakeFiles/fido.dir/BasicGroupBigraph.o.d -o CMakeFiles/fido.dir/BasicGroupBigraph.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8:
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
../src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
../src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:76:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   76 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/ostream:40,
                 from /usr/include/c++/13/iostream:41,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:11:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:99:37: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   99 | struct OrderScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                     ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:108:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  108 | struct OrderScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                          ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:119:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  119 | struct OrderScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:127:38: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  127 | struct UniqueScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                      ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:133:43: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  133 | struct UniqueScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                           ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:139:33: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  139 | struct UniqueScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                 ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 12%] Building CXX object CMakeFiles/fido.dir/BasicBigraph.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/BasicBigraph.o -MF CMakeFiles/fido.dir/BasicBigraph.o.d -o CMakeFiles/fido.dir/BasicBigraph.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.cpp:4:
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
../src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
../src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:76:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   76 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/istream:40,
                 from /usr/include/c++/13/fstream:40,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:4:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:99:37: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   99 | struct OrderScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                     ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:108:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  108 | struct OrderScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                          ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:119:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  119 | struct OrderScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:127:38: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  127 | struct UniqueScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                      ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:133:43: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  133 | struct UniqueScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                           ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:139:33: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  139 | struct UniqueScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                 ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/StringTable.h:9,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:6:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 50%] Building CXX object CMakeFiles/fido.dir/Numerical.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Numerical.o -MF CMakeFiles/fido.dir/Numerical.o.d -o CMakeFiles/fido.dir/Numerical.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 62%] Building CXX object CMakeFiles/fido.dir/Random.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Random.o -MF CMakeFiles/fido.dir/Random.o.d -o CMakeFiles/fido.dir/Random.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Random.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 75%] Building CXX object CMakeFiles/fido.dir/Set.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Set.o -MF CMakeFiles/fido.dir/Set.o.d -o CMakeFiles/fido.dir/Set.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 87%] Building CXX object CMakeFiles/fido.dir/Vector.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Vector.o -MF CMakeFiles/fido.dir/Vector.o.d -o CMakeFiles/fido.dir/Vector.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Vector.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[ 37%] Building CXX object CMakeFiles/fido.dir/GroupPowerBigraph.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/GroupPowerBigraph.o -MF CMakeFiles/fido.dir/GroupPowerBigraph.o.d -o CMakeFiles/fido.dir/GroupPowerBigraph.o -c /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:144,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/GroupPowerBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:119:10: warning: 'Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]' was hidden [-Woverloaded-virtual=]
  119 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.cpp:32:5: warning: 'T& Array<T>::operator[](int) [with T = int]' was hidden [-Woverloaded-virtual=]
   32 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/fido/Set.h:31:15: note:   by 'Set::operator[]'
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/BasicGroupBigraph.h:8:
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder()':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
../src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:58:3: warning:   when initialized here [-Wreorder]
   58 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
../src/Scores.h: In constructor 'ScoreHolder::ScoreHolder(double, int, PSMDescription*)':
../src/Scores.h:55:7: warning: 'ScoreHolder::label' will be initialized after [-Wreorder]
   55 |   int label;
      |       ^~~~~
../src/Scores.h:54:19: warning:   'PSMDescription* ScoreHolder::pPSM' [-Wreorder]
   54 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:59:3: warning:   when initialized here [-Wreorder]
   59 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:76:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   76 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/string:49,
                 from /usr/include/c++/13/bits/locale_classes.h:40,
                 from /usr/include/c++/13/bits/ios_base.h:41,
                 from /usr/include/c++/13/ios:44,
                 from /usr/include/c++/13/ostream:40,
                 from /usr/include/c++/13/iostream:41,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/fido/Array.h:11:
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:99:37: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   99 | struct OrderScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                     ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:108:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  108 | struct OrderScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                          ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:119:32: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  119 | struct OrderScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:127:38: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  127 | struct UniqueScanMassCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                      ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:133:43: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  133 | struct UniqueScanMassLabelCharge : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                           ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
../src/Scores.h:139:33: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  139 | struct UniqueScanLabel : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                 ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[100%] Linking CXX static library libfido.a
/usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/fido.dir/link.txt --verbose=1
/usr/bin/ar qc libfido.a CMakeFiles/fido.dir/BasicBigraph.o CMakeFiles/fido.dir/BasicGroupBigraph.o CMakeFiles/fido.dir/GroupPowerBigraph.o CMakeFiles/fido.dir/Numerical.o CMakeFiles/fido.dir/Random.o CMakeFiles/fido.dir/Set.o CMakeFiles/fido.dir/Vector.o
/usr/bin/ranlib libfido.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
[100%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/fido/CMakeFiles 0
~/build/BUILD/percolator-rel-3-05
+ popd
+ mkdir -p converters
~/build/BUILD/percolator-rel-3-05/converters ~/build/BUILD/percolator-rel-3-05
+ pushd converters
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -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
+ /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -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 -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DPERCOLATOR-CONVERTERS_BINARY_DIR:STATIC=converters -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so -DSERIALIZE=TokyoCabinet -DTARGET_ARCH=s390x ../src/converters
-- The C compiler identification is GNU 13.0.0
-- The CXX compiler identification is GNU 13.0.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR-CONVERTERS:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- Indicate the type of XML serialization scheme : 
		  -DSERIALIZE="Boost" or -DSERIALIZE="TokyoCabinet" 
		  or -DSERIALIZE="LevelDB".
		  By setting up the variable SERIALIZE to either Boost 
		  or TokyoCabinet or LevelDB you will choose the serialization 
		  scheme that will be used to build Converters.
		  Boost serialization option will be used as default if no option is given.
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- XML_SUPPORT = ON
-- PERCOLATOR_SOURCE_DIR = /builddir/build/BUILD/percolator-rel-3-05/src/converters/../..
-- CMAKE_PREFIX_PATH = ../
-- TARGET_ARCH = s390x
-- TOOL CHAIN FILE = 
-- SERIALIZE = TokyoCabinet
-- PROFILING = 
-- Using Tokyo Cabinet Serialization scheme
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages..
-- Found Xerces-C: /usr/lib64/libxerces-c.so
--               : /usr/include
--        Version: 3.2.3
-- Package CodeSynthesis XSD found: /usr/include
-- Found TokyoCabinet: /usr/lib64/libtokyocabinet.so  
-- Package Tokyo Cabinet found : /usr/include
-- Found BZip2: /usr/lib64/libbz2.so  
-- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so - found
-- Bzip2 found
-- Found Boost: /usr/lib64/cmake/Boost-1.78.0/BoostConfig.cmake (found suitable version "1.78.0", minimum required is "1.46.0") found components: filesystem system 
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Generating classes from xsd-schema using CodeSynthesis
-- Generating /builddir/build/BUILD/percolator-rel-3-05/converters/gaml_tandem1.0.cxx;/builddir/build/BUILD/percolator-rel-3-05/converters/gaml_tandem1.0.hxx
-- SQL Lite 3 found: /usr/include
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.13") 
-- ZLIB found: /usr/include, /usr/lib64/libz.so
-- Using FragSpectrumScanDatabaseTokyodb.cpp
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_SKIP_INSTALL_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR


-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-05/converters
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../src/xml/percolator_in.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../src/xml/percolator_out.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://psidev.info/psi/pi/mzIdentML/1.1=mzIdentML_ns ../src/xml/mzIdentML1.1.0.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/gaml_tandem1.0.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.thegpm.org/TANDEM/2011.12.01.1=tandem_ns --namespace-map =tandem_ns --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/tandem2011.12.01.1.xsd
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/converters -B/builddir/build/BUILD/percolator-rel-3-05/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/converters//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
/usr/bin/make  -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/depend
/usr/bin/make  -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake --color=
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake --color=
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/usr/bin/make  -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/build
make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[  3%] Built target generate_perc_xsdfiles
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[  7%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__  -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o -MF CMakeFiles/RAMP.dir/ramp_base64.cpp.o.d -o CMakeFiles/RAMP.dir/ramp_base64.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp_base64.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[  9%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__  -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o -MF CMakeFiles/RAMP.dir/ramp.cpp.o.d -o CMakeFiles/RAMP.dir/ramp.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1698:13: warning: variable 'err' set but not used [-Wunused-but-set-variable]
 1698 |         int err;
      |             ^~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:34:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPFILE* rampOpenFile(const char*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:188:16: note: in expansion of macro 'ramp_fgets'
  188 |         (void) ramp_fgets(buf, sizeof(buf) - 1, result);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'ramp_fileoffset_t getIndexOffset(RAMPFILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:343:3: note: in expansion of macro 'ramp_fread'
  343 |   ramp_fread(indexOffsetTemp, sizeof(indexOffsetTemp), pFI);
      |   ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'ramp_fileoffset_t* readIndex(RAMPFILE*, ramp_fileoffset_t, int*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:509:18: note: in expansion of macro 'ramp_fgets'
  509 |           (void) ramp_fgets(buf, SIZE_BUF, pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:541:18: note: in expansion of macro 'ramp_fgets'
  541 |           (void) ramp_fgets(buf, SIZE_BUF, pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:575:16: note: in expansion of macro 'ramp_fgets'
  575 |         (void) ramp_fgets(buf, SIZE_BUF, pFI);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'void readHeader(RAMPFILE*, ramp_fileoffset_t, ScanHeaderStruct*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:967:18: note: in expansion of macro 'ramp_fgets'
  967 |           (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:984:18: note: in expansion of macro 'ramp_fgets'
  984 |           (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'int readMsLevel(RAMPFILE*, ramp_fileoffset_t)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1056:10: note: in expansion of macro 'ramp_fgets'
 1056 |   (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |          ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1058:12: note: in expansion of macro 'ramp_fgets'
 1058 |     (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |            ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1479:11: note: in expansion of macro 'ramp_fread'
 1479 |           ramp_fread(pData + partial, (int)(peaksLen - partial), pFI);
      |           ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1571:14: note: in expansion of macro 'ramp_fgets'
 1571 |       (void) ramp_fgets(buf, sizeof(buf) - 1, pFI);
      |              ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1573:16: note: in expansion of macro 'ramp_fgets'
 1573 |         (void) ramp_fgets(buf, sizeof(buf) - 1, pFI);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1626:18: note: in expansion of macro 'ramp_fgets'
 1626 |           (void) ramp_fgets(buf, sizeof(buf) - 1 , pFI);
      |                  ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:118:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  118 | #define ramp_fread(buf,len,handle) fread(buf,1,len,(handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1658:9: note: in expansion of macro 'ramp_fread'
 1658 |         ramp_fread(pData + partial, peaksLen - partial, pFI);
      |         ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'void readMSRun(RAMPFILE*, RunHeaderStruct*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1792:10: note: in expansion of macro 'ramp_fgets'
 1792 |   (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |          ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1795:12: note: in expansion of macro 'ramp_fgets'
 1795 |     (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |            ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1816:12: note: in expansion of macro 'ramp_fgets'
 1816 |     (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |            ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'InstrumentStruct* getInstrumentStruct(RAMPFILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1926:10: note: in expansion of macro 'ramp_fgets'
 1926 |   (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |          ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1933:13: note: in expansion of macro 'ramp_fgets'
 1933 |      (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |             ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:119:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  119 | #define ramp_fgets(buf,len,handle) fgets(buf, len, (handle)->fileHandle)
      |                                    ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1989:14: note: in expansion of macro 'ramp_fgets'
 1989 |       (void) ramp_fgets(stringBuf, SIZE_BUF, pFI);
      |              ^~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.h:123:
In function '*strchr',
    inlined from 'readPeaks(RAMPFILE*, long)' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: 'strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |          ~~~~~~~~~~~~~~~~~^~~~~~~~~~
In function 'readPeaks(RAMPFILE*, long)':
cc1plus: note: source object is likely at address zero
In function '*strchr',
    inlined from 'readPeaks(RAMPFILE*, long)' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: 'strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |          ~~~~~~~~~~~~~~~~~^~~~~~~~~~
In function 'readPeaks(RAMPFILE*, long)':
cc1plus: note: source object is likely at address zero
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp: In function 'rampSelfTest(char*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:2050:12: warning: 'strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
 2050 |     strncpy(buf, filename, sizeof(buf));
      |            ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:2054:12: warning: 'strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
 2054 |     strncpy(buf, filename, sizeof(buf));
      |            ^
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/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In constructor 'parser_impl::parser_impl()':
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:106:33: warning: 'parser_impl::gp_' will be initialized after [-Wreorder]
  106 |   std::auto_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
      |                                 ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:102:22: warning:   'xercesc_3_2::DOMImplementation& parser_impl::dom_impl_' [-Wreorder]
  102 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
  144 | parser_impl::parser_impl() : clean_(true),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx: In member function 'xsd::cxx::xml::dom::auto_ptr<xercesc_3_2::DOMDocument> parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:178:14: warning: unused variable 'n' [-Wunused-variable]
  178 |       size_t n(s.size());
      |              ^
/builddir/build/BUILD/percolator-rel-3-05/src/parser.cxx:170:9: warning: unused variable 'i' [-Wunused-variable]
  170 |     int i(1);
      |         ^
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/Reader.cpp.o -MF CMakeFiles/converters.dir/Reader.cpp.o.d -o CMakeFiles/converters.dir/Reader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp: In member function 'Reader::translateFileToXML(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, unsigned int, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp:327:32: warning: 'tcd' may be used uninitialized [-Wmaybe-uninitialized]
  327 |         tmpDirs[lineNumber_par]=tcd;
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Reader.cpp:302:22: note: 'tcd' was declared here
  302 |               char * tcd;
      |                      ^~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/MzidentmlReader.cpp.o -MF CMakeFiles/converters.dir/MzidentmlReader.cpp.o.d -o CMakeFiles/converters.dir/MzidentmlReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp: In member function 'virtual void MzidentmlReader::getMaxMinCharge(const std::string&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp:86:30: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
   86 |   } catch (ifstream::failure e) {
      |                              ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp:94:24: warning: catching polymorphic type 'class MyException' by value [-Wcatch-value=]
   94 |   } catch (MyException e) {
      |                        ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MzidentmlReader.cpp:97:27: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
   97 |   } catch (std::exception e) {
      |                           ^
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[ 41%] Building CXX object CMakeFiles/converters.dir/SqtReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/SqtReader.cpp.o -MF CMakeFiles/converters.dir/SqtReader.cpp.o.d -o CMakeFiles/converters.dir/SqtReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/SqtReader.cpp
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[ 45%] Building CXX object CMakeFiles/converters.dir/SequestReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/SequestReader.cpp.o -MF CMakeFiles/converters.dir/SequestReader.cpp.o.d -o CMakeFiles/converters.dir/SequestReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/SequestReader.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/SequestReader.cpp: In member function 'virtual void SequestReader::createPSM(const mzIdentML_ns::SpectrumIdentificationItemType&, percolatorInNs::fragSpectrumScan::experimentalMass_type, bool, unsigned int, boost::shared_ptr<FragSpectrumScanDatabase>, const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/SequestReader.cpp:169:12: warning: unused variable 'PI' [-Wunused-variable]
  169 |     double PI = boost::lexical_cast<double>(item.calculatedPI().get());
      |            ^~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/SequestReader.cpp:174:14: warning: unused variable 'peptide_length' [-Wunused-variable]
  174 |     unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
      |              ^~~~~~~~~~~~~~
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[ 47%] Building CXX object CMakeFiles/converters.dir/MsgfplusReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/MsgfplusReader.cpp.o -MF CMakeFiles/converters.dir/MsgfplusReader.cpp.o.d -o CMakeFiles/converters.dir/MsgfplusReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp: In member function 'virtual void MsgfplusReader::createPSM(const mzIdentML_ns::SpectrumIdentificationItemType&, percolatorInNs::fragSpectrumScan::experimentalMass_type, bool, unsigned int, boost::shared_ptr<FragSpectrumScanDatabase>, const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:333:27: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
  333 |                           else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
      |                           ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:333:104: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
  333 |                           else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
      |                                                                                                        ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:272:14: warning: unused variable 'peptide_length' [-Wunused-variable]
  272 |     unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
      |              ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MsgfplusReader.cpp:291:12: warning: variable 'SpecEValue' set but not used [-Wunused-but-set-variable]
  291 |     double SpecEValue = 0.0;
      |            ^~~~~~~~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabase.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabase.cpp: In member function 'std::string FragSpectrumScanDatabase::decoratePeptide(const percolatorInNs::peptideType&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabase.cpp:80:19: warning: comparison of integer expressions of different signedness: 'const int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   80 |     if (it->first <= peptideSeq.length()) {
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/TandemReader.cpp.o -MF CMakeFiles/converters.dir/TandemReader.cpp.o.d -o CMakeFiles/converters.dir/TandemReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp: In member function 'virtual void TandemReader::getMaxMinCharge(const std::string&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp:274:24: warning: catching polymorphic type 'class MyException' by value [-Wcatch-value=]
  274 |   } catch (MyException e) {
      |                        ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp:277:27: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
  277 |   } catch (std::exception e) {
      |                           ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp: In member function 'void TandemReader::createPSM(const tandem_ns::peptide::domain_type&, double, unsigned int, double, double, bool, boost::shared_ptr<FragSpectrumScanDatabase>, const peptideProteinMapType&, const std::string&, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/TandemReader.cpp:497:29: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
  497 |     f_seq.push_back( charge == c ? 1.0 : 0.0);
      |                      ~~~~~~~^~~~
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/builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabaseTokyodb.cpp: In member function 'virtual void FragSpectrumScanDatabaseTokyoDB::putFSS(percolatorInNs::fragSpectrumScan&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/FragSpectrumScanDatabaseTokyodb.cpp:165:10: warning: unused variable 'valueSize' [-Wunused-variable]
  165 |   size_t valueSize(buf.size ());
      |          ^~~~~~~~~
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In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.h: In constructor 'Interface::Interface()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.h:50:14: warning: 'Interface::xmlOutput' will be initialized after [-Wreorder]
   50 |         bool xmlOutput;
      |              ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.h:47:21: warning:   'std::string Interface::outputFN' [-Wreorder]
   47 |         std::string outputFN;
      |                     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/Interface.cpp:21:1: warning:   when initialized here [-Wreorder]
   21 | Interface::Interface() : xmlOutput(false), outputFN("") { }
      | ^~~~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o -MF CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o.d -o CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp
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/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In function 'LazyMatrix* flip_lazy_matrix(LazyMatrix&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:21:30: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   21 |         for ( uint j = 0 ; j < lm.rows() ; j++ ) {
      |                            ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:22:38: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
   22 |                 for ( uint i = 0 ; i < lm.cols() ; i++ ) {
      |                                    ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In copy constructor 'LazyMatrix::LazyMatrix(const self&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:56:6: warning: value computed is not used [-Wunused-value]
   56 |      *data_copies++;
      |      ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::copy_m_flip(const self&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:67:28: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'const int' [-Wsign-compare]
   67 |       for ( uint i = 0 ; i < x.nrows ; i++ ) {
      |                          ~~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::to_full_data(bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:101:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float>*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  101 |           for ( int i = 0 ; i < m.size() ; i++ ) {
      |                             ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::to_full_data(value_type, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:115:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float>*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  115 |           for ( int i = 0 ; i < m.size() ; i++ ) {
      |                             ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::_get_row_retain(std::vector<float>&, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:179:43: warning: variable 'b' set but not used [-Wunused-but-set-variable]
  179 |              std::vector<float>::iterator b = this->m[i]->begin();
      |                                           ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::add_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:313:31: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  313 |          for ( uint i = 0 ; i < nrows ; i++ ) {
      |                             ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::mult_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:322:31: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  322 |          for ( uint i = 0 ; i < nrows ; i++ ) {
      |                             ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::div_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:331:31: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  331 |          for ( uint i = 0 ; i < nrows ; i++ ) {
      |                             ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::set_min_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:339:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  339 |     for ( uint i = 0 ; i < nrows ; i++ ) {
      |                        ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::set_max_val(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:351:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  351 |     for ( uint i = 0 ; i < nrows ; i++ ) {
      |                        ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::column_shift(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:369:23: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  369 |   for ( uint i = 0 ;i < rows() ; i++ ) {
      |                     ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:370:26: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  370 |     for ( uint j = 0 ; j < cols() ; j++ ) {
      |                        ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:373:21: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  373 |       if ( dest_idx >= cols() ) break;
      |            ~~~~~~~~~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp: In member function 'void LazyMatrix::linear_shift(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:389:25: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  389 |     for ( uint i = 0; i < shift ; i++ ) {
      |                       ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:393:29: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  393 |     for ( uint i = shift; i < nrows; i++ ) {
      |                           ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/LazyMatrix.cpp:412:39: warning: comparison of integer expressions of different signedness: 'uint' {aka 'unsigned int'} and 'int' [-Wsign-compare]
  412 |     for ( uint i = nrows - offset ; i < nrows; i++ ) {
      |                                     ~~^~~~~~~
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cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o -MF CMakeFiles/MSToolkit.dir/MSObject.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSObject.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp
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/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp: In copy constructor 'MSObject::MSObject(const MSObject&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp:21:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Spectrum>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   21 |   for(i=0;i<m.vSpectrum->size();i++){
      |           ~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp: In member function 'MSObject& MSObject::operator=(const MSObject&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSObject.cpp:36:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Spectrum>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   36 |     for(i=0;i<m.vSpectrum->size();i++){
      |             ~^~~~~~~~~~~~~~~~~~~~
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[ 70%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o -MF CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSSingleScan.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 72%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o -MF CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp
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/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp: In function 'int main(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp:51:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   51 |   for ( int i = 0 ; i < rts.size() ; i++ ) {
      |                     ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTAllRT.cpp:26:22: warning: variable 'ff' set but not used [-Wunused-but-set-variable]
   26 |         MSFileFormat ff;
      |                      ^~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 69%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o -MF CMakeFiles/MSToolkit.dir/MSReader.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::writeSqlite(const char*, MSObject&, char*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:634:34: warning: the address of 'MSHeader::header' will never be NULL [-Waddress]
  634 |       if(m.getHeader().header[i] != 0)
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.h:4,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.h:4,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSToolkitTypes.h:54:14: note: 'MSHeader::header' declared here
   54 |         char header[16][128];
      |              ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::appendFile(Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:916:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  916 |           for(int i=0; i<chgs.size(); i++)
      |                        ~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:750:7: warning: variable 'err' set but not used [-Wunused-but-set-variable]
  750 |   int err;
      |       ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:756:9: warning: variable 'sizeM' set but not used [-Wunused-but-set-variable]
  756 |   uLong sizeM;
      |         ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:757:9: warning: variable 'sizeI' set but not used [-Wunused-but-set-variable]
  757 |   uLong sizeI;
      |         ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'bool MSReader::executeSqlStmt(Spectrum&, char*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1187:7: warning: unused variable 'charge' [-Wunused-variable]
 1187 |   int charge=-1;
      |       ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::writeCompressSpec(FILE*, Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1610:13: warning: variable 'err' set but not used [-Wunused-but-set-variable]
 1610 |         int err;
      |             ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1616:15: warning: variable 'sizeM' set but not used [-Wunused-but-set-variable]
 1616 |         uLong sizeM;
      |               ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1617:15: warning: variable 'sizeI' set but not used [-Wunused-but-set-variable]
 1617 |         uLong sizeI;
      |               ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'int MSReader::openFile(const char*, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:101:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  101 |       fread(&iFType,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:102:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  102 |       fread(&iVersion,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:103:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  103 |                         fread(&header,sizeof(MSHeader),1,fileIn);
      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'bool MSReader::readFile(const char*, bool, Spectrum&, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:189:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  189 |                 fread(&i,4,1,fileIn);
      |                 ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:191:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  191 |                 fread(&i,4,1,fileIn);
      |                 ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:207:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  207 |       fread(&z.z,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:208:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  208 |       fread(&z.mz,8,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:213:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  213 |       fread(&ez.z,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:214:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  214 |       fread(&ez.mh,8,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:215:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  215 |       fread(&ez.pRTime,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:216:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  216 |       fread(&ez.pArea,4,1,fileIn);
      |       ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:239:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  239 |               fread(&p.mz,8,1,fileIn);
      |               ~~~~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:240:20: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  240 |               fread(&p.intensity,4,1,fileIn);
      |               ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:280:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  280 |               fgets(tstr,256,fileIn);
      |               ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:285:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  285 |               fgets(tstr,256,fileIn);
      |         make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
      ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:297:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  297 |         fgets(tstr,256,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:347:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  347 |                 fgets(tstr,256,fileIn);
      |                 ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:374:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  374 |                 fgets(tstr,256,fileIn);
      |                 ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:377:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  377 |               fgets(tstr,256,fileIn);
      |               ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:400:24: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  400 |                   fgets(tstr,256,fileIn);
      |                   ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:405:21: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
  405 |               fscanf(fileIn,"%lf %f\n",&p.mz,&p.intensity);
      |               ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:411:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  411 |         fgets(tstr,256,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::readCompressSpec(FILE*, MSScanInfo&, Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1669:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1669 |         fread(&i,4,1,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1671:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1671 |         fread(&i,4,1,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1677:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1677 |         fread(compr,mzLen,1,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1684:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1684 |         fread(compr,intensityLen,1,fileIn);
      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'void MSReader::readSpecHeader(FILE*, MSScanInfo&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1882:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1882 |   fread(&ms.scanNumber[0],4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1884:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1884 |   fread(&ms.scanNumber[1],4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1885:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1885 |   fread(&ms.mz,8,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1886:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1886 |   fread(&ms.rTime,4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1889:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1889 |     fread(&ms.BPI,4,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1890:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1890 |     fread(&ms.BPM,8,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1891:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1891 |     fread(&ms.convA,8,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1892:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1892 |     fread(&ms.convB,8,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1893:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1893 |     fread(&ms.TIC,8,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1894:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1894 |     fread(&ms.IIT,4,1,fileIn);
      |     ~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1897:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1897 |   fread(&ms.numZStates,4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1899:24: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1899 |   if(iVersion>=3) fread(&ms.numEZStates,4,1,fileIn);
      |                   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1902:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1902 |   fread(&ms.numDataPoints,4,1,fileIn);
      |   ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'MSFileFormat MSReader::checkFileFormat(const char*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1952:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1952 |   fread(&i,4,1,f);
      |   ~~~~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:1953:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
 1953 |   fread(&iVersion,4,1,f);
      |   ~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:906,
                 from /usr/include/c++/13/cstdio:42,
                 from /usr/include/c++/13/parallel/compiletime_settings.h:33,
                 from /usr/include/c++/13/parallel/parallel.h:37,
                 from /usr/include/c++/13/parallel/base.h:40,
                 from /usr/include/c++/13/parallel/algobase.h:40,
                 from /usr/include/c++/13/bits/stl_algobase.h:2229,
                 from /usr/include/c++/13/vector:62,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.h:5:
In function 'sprintf',
    inlined from 'MSReader::appendFile(Spectrum&)' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:869:11:
/usr/include/bits/stdio2.h:30:34: warning: 'lastScanID' may be used uninitialized [-Wmaybe-uninitialized]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp: In member function 'MSReader::appendFile(Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSReader.cpp:853:7: note: 'lastScanID' was declared here
  853 |   int lastScanID;
      |       ^~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 74%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o -MF CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSTDemo.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 78%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o -MF CMakeFiles/MSToolkit.dir/Spectrum.cpp.o.d -o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'Spectrum& Spectrum::operator=(const Spectrum&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:81:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   81 |     for(i=0;i<s.vPeaks->size();i++){
      |             ~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:85:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<EZState>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   85 |     for(i=0;i<s.vEZ->size();i++){
      |             ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:89:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<ZState>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   89 |     for(i=0;i<s.vZ->size();i++){
      |             ~^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'bool Spectrum::getRawFilter(char*, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:282:8: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  282 |   if(sz<strlen(rawFilter)) {
      |      ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'float Spectrum::getTotalIntensity()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:389:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  389 |   for(int i=0; i<vPeaks->size(); i++)
      |                ~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'void Spectrum::setPeaks(std::vector<Peak_T>)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:428:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  428 |   for(int i=0; i<peaks.size(); i++)
      |                ~^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp: In member function 'void Spectrum::printMe()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/Spectrum.cpp:453:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Peak_T>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  453 |   for(int i=0; i<vPeaks->size(); i++)
      |                ~^~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 76%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o -MF CMakeFiles/MSToolkit.dir/MSWarper.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp:17:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
  517 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
  519 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable]
  600 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
  703 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp: In function 'int main(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSWarper.cpp:87:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<const char*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   87 |   for ( int f_idx = 0; f_idx < ms1_file_names.size() ; f_idx++ ) {
      |                        ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
  812 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
  813 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
  814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
  815 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
  818 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
  819 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:820:16: warning: 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)' declared 'static' but never defined [-Wunused-function]
  820 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
      |                ^~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:48:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 81%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:17:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
  517 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
  519 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable]
  600 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
  703 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'std::vector<transition_info> transition_manager::get_trans_by_precursor(float)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:37:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   37 |        for ( int i = 0 ; i < precursors.size() ; i++ )
      |                          ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'std::vector<transition_info> transition_manager::get_trans_by_precursor_idx(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:48:29: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<transition_info>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   48 |         for ( int i = 0 ; i < ti.size() ; i++ ) {
      |                           ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In constructor 'transition_manager::transition_manager(std::vector<transition_info>)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:57:28: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<transition_info>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   57 |       for ( int  i = 0 ; i < transitions.size() ; i++ ) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::init_transitions_from_labels()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:86:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   86 |    for ( int i = 0 ; i < labels.size() ; i++ ) {
      |                      ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::tabular_input(std::ifstream&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:119:36: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  119 |      for ( int mz_idx = 0 ; mz_idx < this->get_num_mzs() ; mz_idx++ ) {
      |                             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:120:38: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  120 |          for ( int c_idx = 0 ; c_idx < this->get_num_rts() ; c_idx++ ) {
      |                                ~~~~~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:117:10: warning: unused variable 'num_chroms' [-Wunused-variable]
  117 |      int num_chroms = this->get_num_mzs();
      |          ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:118:10: warning: unused variable 'num_rts' [-Wunused-variable]
  118 |      int num_rts = this->get_num_rts();
      |          ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_dist_set(int, std::vector<int>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:228:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  228 |     for ( int i = 0 ; i < this->get_num_rts() ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_chrom_set(int, std::vector<std::pair<int, int> >&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:247:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  247 |     for ( int i = 1 ; i < retain_range.size() ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:255:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  255 |     for ( int i = 0 ; i < delete_range.size() ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:237:9: warning: unused variable 'set_idx' [-Wunused-variable]
  237 |     int set_idx = 0;
      |         ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::retain_chrom(int, int, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:266:39: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  266 |   for ( int i = stop_scan_idx + 1 ; i < get_num_rts() ; i++ ) {
      |                                     ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'int msmat::check_size_from_position() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:283:30: warning: comparison of integer expressions of different signedness: 'off64_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  283 |   if ( ( end_pos - cur_pos ) == get_num_mzs() * get_num_rts() * sizeof(float) ) {
      |        ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'int msmat::rt_to_rtidx(float) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:417:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  417 |      if ( iter_delt == rts.size() - 1 )
      |           ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::calc_bp_chrom()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:680:28: warning: variable 'scan_length' set but not used [-Wunused-but-set-variabmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
le]
  680 |   int scan_idx, num_scans, scan_length;
      |                            ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::time_interpolate(double, msmat&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1068:14: warning: variable 'dim' set but not used [-Wunused-but-set-variable]
 1068 |   matrix_dim dim = get_data_dim();
      |              ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::get_median() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1278:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1278 |   for ( int i = 0 ; i < this->get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1279:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1279 |     for ( int j = 0 ; j < this->get_num_cols() ; j++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::get_avg(int) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1294:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1294 |     if ( i < 0 || i >= get_num_rts()  ) {
      |                   ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::calc_twomat_num(const msmat&, double, double, int) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1325:72: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1325 |                                      for ( int self_idx = 0 ; self_idx < get_num_rts() ; self_idx++ ) {
      |                                                               ~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1327:72: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1327 |                                        if ( other_idx < 0 || other_idx >= other.get_num_rts() ) {
      |                                                              ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::calc_mat_denom(double, int) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1350:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1350 |     if ( i < 0 || i >= get_num_rts() ) {
      |                   ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::correlation_w_shift(const msmat&, int) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1368:17: warning: unused variable 'self' [-Wunused-variable]
 1368 |   const msmat & self = *this;
      |                 ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'msmat_chroms* msmat_chroms::extract_mzidx_range(int, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1422:9: warning: unused variable 'foo' [-Wunused-variable]
 1422 |     int foo = 5;
      |         ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_scans::get_chrom(int, std::vector<float>&) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1498:11: warning: unused variable 'volatile_this' [-Wunused-variable]
 1498 |   msmat * volatile_this;
      |           ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::scan_scramble()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1555:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1555 |   for ( int i = 0 ; i < get_num_rts() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1561:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<int, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1561 |   for ( int i = 0 ; i < scram_cmds.size() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In function 'msmat* test_msmat(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1605:19: warning: variable 'ti_file' set but not used [-Wunused-but-set-variable]
 1605 |   FILE * o_file, *ti_file, *sg_file;
      |                   ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1605:29: warning: variable 'sg_file' set but not used [-Wunused-but-set-variable]
 1605 |   FILE * o_file, *ti_file, *sg_file;
      |                             ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In function 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1746:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1746 |   for ( int i = 0 ; i < chroms.size() ; i++ ){
      |                     ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1762:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<float> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1762 |   for ( int i = 0 ; i < chroms.size() ; i++ ){
      |                     ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_mzs_by_avg(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1828:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1828 |     new_cnt < mzs.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_rts_by_avg(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1858:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1858 |     new_cnt < rts.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_mzs_by_sample(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1880:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1880 |     new_cnt < mzs.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::decimate_rts_by_sample(int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1898:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 1898 |     new_cnt < rts.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'bool msmat::equals_data(const msmat&, double) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1921:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1921 |   for ( int i = 0 ; i < get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'double msmat::sum_abs_diffs(const msmat&) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1944:23: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
 1944 |   for ( int i = 0 ; i < get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1941:10: warning: unused variable 'nrows' [-Wunused-variable]
 1941 |   size_t nrows = get_num_rows();
      |          ^~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void msmat::tabular_output(std::ostream&, int, int, int, int, bool, char)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2004:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2004 |     for ( int i = 0 ; i < rts_slice.size() - 1 ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2010:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2010 |   for ( int i = 0 ; i < mzs_slice.size() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2019:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2019 |     for ( int j = 0 ; j < out_chrom.size() - 1 ; j++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1990:13: warning: unused variable 'num_mzs' [-Wunused-variable]
 1990 |   const int num_mzs = get_num_mzs();
      |             ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_scans::get_scan_interp(float, std::vector<float>&) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2071:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2071 |   for ( int i = 0 ; i < s1.size() ;i++ ) {
      |                     ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'virtual void msmat_chroms::get_scan_interp(float, std::vector<float>&) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2095:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<float>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
 2095 |   for ( int i = 0 ; i < s1.size() ;i++ ) {
      |                     ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp: In member function 'void ttest_score_matrix::unmask_search(msmat::mz_type, msmat::rt_type, msmat::rt_type)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2109:7: warning: unused variable 'start_rt_idx' [-Wunused-variable]
 2109 |   int start_rt_idx = this->rt_to_rtidx(start_rt);
      |       ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:2110:7: warning: unused variable 'stop_rt_idx' [-Wunused-variable]
 2110 |   int stop_rt_idx = this->rt_to_rtidx(stop_rt);
      |       ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
  812 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
  813 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
  814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1740:9: warning: 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)' defined but not used [-Wunused-function]
 1740 | msmat * msmat_from_thevoid
      |         ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1713:6: warning: 'void output_bp_chrom(msmat&, char*)' defined but not used [-Wunused-function]
 1713 | void output_bp_chrom( msmat & m, char * fname  ) {
      |      ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.cpp:1582:9: warning: 'msmat* test_msmat(int, char**)' defined but not used [-Wunused-function]
 1582 | msmat * test_msmat ( int argc , char ** argv ) {
      |         ^~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:48:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 83%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_base.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.cpp:16:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 85%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:20:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
  517 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
  519 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable]
  600 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
  703 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'int msmat_header_parser::read_header(msmat*, FILE*, bool, int*)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:92:14: warning: unused variable 'should_be_semi' [-Wunused-variable]
   92 |         char should_be_semi = (char)fgetc(header_fh);
      |              ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'void msmat_header_parser::load_strmap_from_str(std::map<std::__cxx11::basic_string<char>, float>&, const char*, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:343:22: warning: unused variable 'key_fields_len' [-Wunused-variable]
  343 |   int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |                      ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:343:38: warning: unused variable 'key_last_loc' [-Wunused-variable]
  343 |   int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |                                      ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:343:52: warning: unused variable 'key_data_len' [-Wunused-variable]
  343 |   int c1_loc, c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |                                                    ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:344:8: warning: unused variable 'key_len_data' [-Wunused-variable]
  344 |   char key_len_data[128], val_len_data[128];
      |        ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:344:27: warning: unused variable 'val_len_data' [-Wunused-variable]
  344 |   char key_len_data[128], val_len_data[128];
      |                           ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:367:7: warning: unused variable 'key_data_idx' [-Wunused-variable]
  367 |   int key_data_idx;
      |       ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'void msmat_header_parser::write_header_field_string_list(FILE*, const char*, const std::vector<std::__cxx11::basic_string<char> >&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:431:9: warning: unused variable 'num_elements' [-Wunused-variable]
  431 |     int num_elements = s.size();
      |         ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
  812 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
  813 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
  814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
  815 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
  818 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
  819 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:820:16: warning: 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)' declared 'static' but never defined [-Wunused-function]
  820 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
      |                ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'msmat_header_parser::load_map_from_str(std::map<float, float, std::less<float>, std::allocator<std::pair<float const, float> > >&, char const*, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:314:10: warning: 'operator delete(void*, unsigned long)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  314 |   delete k;
      |          ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:306:48: note: returned from 'operator new[](unsigned long)'
  306 |   flt_map_type * k = new flt_map_type[num_items];
      |                                                ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:315:10: warning: 'operator delete(void*, unsigned long)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  315 |   delete v;
      |          ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:307:48: note: returned from 'operator new[](unsigned long)'
  307 |   flt_map_type * v = new flt_map_type[num_items];
      |                                                ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp: In member function 'msmat_header_parser::load_strmap_from_str(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, float, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::almake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
locator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, float> > >&, char const*, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:394:10: warning: 'operator delete(void*, unsigned long)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  394 |   delete values;
      |          ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_header_parser.cpp:389:37: note: returned from 'operator new[](unsigned long)'
  389 |   float * values = new float[val_len];
      |                                     ^
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 80%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o -MF CMakeFiles/MSToolkit.dir/crawutils.cpp.o.d -o CMakeFiles/MSToolkit.dir/crawutils.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'void crawutils::rankties(std::vector<float>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:261:9: warning: unused variable 'start_idx' [-Wunused-variable]
  261 |     int start_idx = -1;
      |         ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:262:9: warning: unused variable 'stop_idx' [-Wunused-variable]
  262 |     int stop_idx = -1;
      |         ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'void crawutils::rank_by_pos_ties(const std::vector<std::pair<float, int> >&, std::vector<float>&, bool)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:354:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::pair<float, int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  354 |       if ( ( i != (sorted_by_i.size() ) ) && ( sorted_by_i[i].first == last_val) ) {
      |              ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:346:9: warning: unused variable 'last_rank' [-Wunused-variable]
  346 |     int last_rank = -1;
      |         ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::idx_of_centroid(const std::vector<float>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:944:32: warning: comparison of integer expressions of different signedness: 'std::vector<float>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  944 |     if (cumulative_area.size() == idx)
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::idx_of_centroid(const std::vector<float>&, const std::vector<float>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:990:32: warning: comparison of integer expressions of different signedness: 'std::vector<float>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  990 |     if (cumulative_area.size() == idx)
      |         ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'int crawutils::tryptic_digester_proto(std::string, std::vector<std::__cxx11::basic_string<char> >&, int)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:1121:10: warning: unused variable 'last_tryp' [-Wunused-variable]
 1121 |     bool last_tryp = false;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp: In function 'std::vector<std::pair<std::set<int>, std::set<int> > > crawutils::permute_two_groups(IdxGroupType, IdxGroupType)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/crawutils.cpp:1214:8: warning: unused variable 'g2_len' [-Wunused-variable]
 1214 |    int g2_len = g2.size();
      |        ^~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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[ 87%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o -MF CMakeFiles/MSToolkit.dir/msmat_test.cpp.o.d -o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp:4:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'std::pair<float, float> msmat::get_transition_by_idx() const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:517:3: warning: no return statement in function returning non-void [-Wreturn-type]
  517 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In member function 'int msmat::get_idx_by_transition(std::pair<float, float>) const':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:519:3: warning: no return statement in function returning non-void [-Wreturn-type]
  519 |   }
      |   ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_scans::msmat_scans()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:600:15: warning: unused variable 'a' [-Wunused-variable]
  600 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: In constructor 'msmat_chroms::msmat_chroms()':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:703:9: warning: unused variable 'a' [-Wunused-variable]
  703 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp: In function 'int main(int, char**)':
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_test.cpp:13:12: warning: unused variable 'm' [-Wunused-variable]
   13 |   msmat  * m;
      |            ^
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:812:12: warning: 'int test_msmat_time_interp(msmat*)' declared 'static' but never defined [-Wunused-function]
  812 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:813:12: warning: 'int test_msmat_sg_test(msmat*)' declared 'static' but never defined [-Wunused-function]
  813 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:814:12: warning: 'int test_msmat_output(msmat*, char*)' declared 'static' but never defined [-Wunused-function]
  814 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:815:16: warning: 'msmat* test_msmat(int, char**)' declared 'static' but never defined [-Wunused-function]
  815 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:818:13: warning: 'void output_bp_chrom(msmat&, char*)' declared 'static' but never defined [-Wunused-function]
  818 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:819:17: warning: 'msmat* msmat_from_fh(FILE*, sparse_level)' declared 'static' but never defined [-Wunused-function]
  819 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:820:16: warning: 'msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)' declared 'static' but never defined [-Wunused-function]
  820 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
      |                ^~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat.H:48:
/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/msmat_base.H:69:21: warning: 'valid_fields' defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/cmake -P CMakeFiles/MSToolkit.dir/cmake_clean_target.cmake
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -MF CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o.d -o CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Sqt2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 92%] Building CXX object CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -MF CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o.d -o CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Msgfplus2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 94%] Linking CXX executable sqt2pin
/usr/bin/cmake -E cmake_link_script CMakeFiles/sqt2pin.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -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 -Wl,-z,relro   -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 -ltirpc -rdynamic CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -o sqt2pin   -L/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src  libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
In function 'strchr',
    inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function 'readPeaks':
lto1: note: source object is likely at address zero
In function 'strchr',
    inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function 'readPeaks':
lto1: note: source object is likely at address zero
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 96%] Built target sqt2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 98%] Building CXX object CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-05/converters -I/builddir/build/BUILD/percolator-rel-3-05/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -MF CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o.d -o CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/Tandem2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 96%] Linking CXX executable msgf2pin
/usr/bin/cmake -E cmake_link_script CMakeFiles/msgf2pin.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -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 -Wl,-z,relro   -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 -ltirpc -rdynamic CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -o msgf2pin   -L/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src  libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
In function 'strchr',
    inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function 'readPeaks':
lto1: note: source object is likely at address zero
In function 'strchr',
    inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function 'readPeaks':
lto1: note: source object is likely at address zero
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[100%] Built target msgf2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[100%] Linking CXX executable tandem2pin
/usr/bin/cmake -E cmake_link_script CMakeFiles/tandem2pin.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -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 -Wl,-z,relro   -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 -ltirpc -rdynamic CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -o tandem2pin   -L/builddir/build/BUILD/percolator-rel-3-05/src/converters/../../src  libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
In function 'strchr',
    inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function 'readPeaks':
lto1: note: source object is likely at address zero
In function 'strchr',
    inlined from 'readPeaks' at /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: '__builtin_strchr' reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function 'readPeaks':
lto1: note: source object is likely at address zero
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-05
+ mkdir -p elude
+ pushd elude
~/build/BUILD/percolator-rel-3-05/elude ~/build/BUILD/percolator-rel-3-05
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -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
+ /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -Wno-dev -DCMAKE_COLOR_MAKEFILE:BOOL=ON -DCMAKE_VERBOSE_MAKEFILE=TRUE -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DCMAKE_PREFIX_PATH:STRING=/usr -DBoost_USE_STATIC_LIBS:BOOL=OFF -DCMAKE_USE_RELATIVE_PATHS:BOOL=ON '-DCMAKE_CXX_FLAGS_RELEASE:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -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 -ltirpc' -DTARGET_ARCH=s390x ../src/elude_tool
-- The C compiler identification is GNU 13.0.0
-- The CXX compiler identification is GNU 13.0.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- 
-- -------------------------------------------------------------------------------
-- Building ELUDE:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- PERCOLATOR_SOURCE_DIR = /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../..
-- CMAKE_PREFIX_PATH = /usr
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = s390x
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Found Boost: /usr/lib64/cmake/Boost-1.78.0/BoostConfig.cmake (found version "1.78.0")  
-- Configuring done
-- Generating done
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/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o -MF CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o.d -o CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionFeatures.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
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/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionFeatures.cpp:304:21: warning: unused variable 'len' [-Wunused-variable]
  304 |   int end_position, len = peptide.size();
      |                     ^~~
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/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o -MF CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o.d -o CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:27:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h: In member function 'bool LibSVRModel::IsModelNull() const':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: second operand of conditional expression has no effect [-Wunused-value]
   57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
      |                                                                 ^
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: third operand of conditional expression has no effect [-Wunused-value]
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:67: warning: no return statement in function returning non-void [-Wreturn-type]
   57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
      |                                                                   ^
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'virtual int LibSVRModel::LoadModel(FILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:284:1: warning: control reaches end of non-void function [-Wreturn-type]
  284 | }
      | ^
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateLinearModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:204:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized]
  204 |   svr_parameters_.C = best_c;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:10: note: 'best_c' was declared here
  182 |   double best_c, best_e;
      |          ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:205:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized]
  205 |   svr_parameters_.p = best_e;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:18: note: 'best_e' was declared here
  182 |   double best_c, best_e;
      |                  ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateRBFModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:240:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized]
  240 |   svr_parameters_.C = best_c;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:10: note: 'best_c' was declared here
  213 |   double best_c, best_e, best_g;
      |          ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:241:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized]
  241 |   svr_parameters_.p = best_e;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:18: note: 'best_e' was declared here
  213 |   double best_c, best_e, best_g;
      |                  ^~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:242:25: warning: 'best_g' may be used uninitialized [-Wmaybe-uninitialized]
  242 |   svr_parameters_.gamma = best_g;
      |   ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:26: note: 'best_g' was declared here
  213 |   double best_c, best_e, best_g;
      |                          ^~~~~~
In member function 'LibSVRModel::CalibrateRBFModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
    inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:255:29:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:240:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized]
  240 |   svr_parameters_.C = best_c;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:10: note: 'best_c' was declared here
  213 |   double best_c, best_e, best_g;
      |          ^~~~~~
In member function 'LibSVRModel::CalibrateRBFModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
    inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:255:29:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:241:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized]
  241 |   svr_parameters_.p = best_e;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:18: note: 'best_e' was declared here
  213 |   double best_c, best_e, best_g;
      |                  ^~~~~~
In member function 'LibSVRModel::CalibrateRBFModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
    inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:255:29:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:242:25: warning: 'best_g' may be used uninitialized [-Wmaybe-uninitialized]
  242 |   svr_parameters_.gamma = best_g;
      |   ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:213:26: note: 'best_g' was declared here
  213 |   double best_c, best_e, best_g;
      |                          ^~~~~~
In member function 'LibSVRModel::CalibrateLinearModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
    inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:253:32:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:204:21: warning: 'best_c' may be used uninitialized [-Wmaybe-uninitialized]
  204 |   svr_parameters_.C = best_c;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:10: note: 'best_c' was declared here
  182 |   double best_c, best_e;
      |          ^~~~~~
In member function 'LibSVRModel::CalibrateLinearModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)',
    inlined from 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)' at /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:253:32:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:205:21: warning: 'best_e' may be used uninitialized [-Wmaybe-uninitialized]
  205 |   svr_parameters_.p = best_e;
      |   ~~~~~~~~~~~~~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp: In member function 'LibSVRModel::CalibrateModel(std::vector<PSMDescription*, std::allocator<PSMDescription*> > const&, int const&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.cpp:182:18: note: 'best_e' was declared here
  182 |   double best_c, best_e;
      |                  ^~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
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/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o -MF CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o.d -o CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibsvmWrapper.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibsvmWrapper.cpp: In function 'svm_model* libsvm_wrapper::LoadModel(FILE*)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibsvmWrapper.cpp:172:7: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
  172 |   int ret;
      |       ^~~
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/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o -MF CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o.d -o CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:17:1: warning: "/*" within comment [-Wcomment]
   17 | /*
      |  
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:27:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h: In member function 'bool LibSVRModel::IsModelNull() const':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: second operand of conditional expression has no effect [-Wunused-value]
   57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
      |                                                                 ^
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:65: warning: third operand of conditional expression has no effect [-Wunused-value]
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LibSVRModel.h:57:67: warning: no return statement in function returning non-void [-Wreturn-type]
   57 |    inline bool IsModelNull() const { svr_ == NULL ? true : false; }
      |                                                                   ^
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:24:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.h: In constructor 'RetentionModel::RetentionModel(Normalizer*)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.h:99:16: warning: 'RetentionModel::the_normalizer_' will be initialized after [-Wreorder]
   99 |    Normalizer *the_normalizer_;
      |                ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.h:95:14: warning:   'SVRModel* RetentionModel::svr_model_' [-Wreorder]
   95 |    SVRModel *svr_model_;
      |              ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:30:1: warning:   when initialized here [-Wreorder]
   30 | RetentionModel::RetentionModel(Normalizer *norm) : the_normalizer_(norm),
      | ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In destructor 'RetentionModel::~RetentionModel()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:36:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
   36 |     delete svr_model_;
      |     ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'void RetentionModel::PrintSub()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:62:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   62 |   for(int i = 0; i < vsub_.size(); ++i)
      |                  ~~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::TrainRetentionModel(const std::set<std::__cxx11::basic_string<char> >&, const std::map<std::__cxx11::basic_string<char>, double>&, bool, std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:187:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
  187 |     delete svr_model_;
      |     ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::SaveModelToFile(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:291:20: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
  291 |   if (vsub_.size() !=  number_features) {
      |       ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp: In member function 'int RetentionModel::LoadModelFromFile(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:356:5: warning: deleting object of abstract class type 'SVRModel' which has non-virtual destructor will cause undefined behavior [-Wdelete-non-virtual-dtor]
  356 |     delete svr_model_;
      |     ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionModel.cpp:363:24: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
  363 |   int number_features, ret;
      |                        ^~~
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/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/DataManager.cpp.o -MF CMakeFiles/eludelibrary.dir/DataManager.cpp.o.d -o CMakeFiles/eludelibrary.dir/DataManager.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp: In static member function 'static std::vector<std::pair<PSMDescription*, std::__cxx11::basic_string<char> > > DataManager::RemoveInSourceFragments(const Enzyme*, const double&, const std::map<std::__cxx11::basic_string<char>, double>&, bool, std::vector<PSMDescription*>&, std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp:334:50: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<PSMDescription*>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  334 |     if (!remove_from_test && (initial_train_size != train_psms.size())) {
      |                               ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp: In static member function 'static std::vector<PSMDescription*> DataManager::RemoveNonEnzymatic(const Enzyme*, std::vector<PSMDescription*>&, const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/DataManager.cpp:354:7: warning: unused variable 'initial_size' [-Wunused-variable]
  354 |   int initial_size = psms.size();
      |       ^~~~~~~~~~~~
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/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::setData(std::vector<double>&, std::vector<double>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:48:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   48 |   for (int i = 0; i < x.size(); ++i) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::fillResiduals(std::pair<double, double>)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:84:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<dataPoint>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   84 |   for (int i = 0; i < data.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::runLTS()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:168:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  168 |         for (int i = 1; i < Q.size(); ++i)
      |                         ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:177:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<dataPoint> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  177 |   for (int j = 0; j < best10Subsets.size(); ++j) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::printVector(std::vector<dataPoint>)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:209:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<dataPoint>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  209 |   for (int i = 0; i < v.size(); ++i) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp: In member function 'void LTSRegression::printDataPoints()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp:220:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<dataPoint>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  220 |   for (int i = h; i < data.size(); ++i) {
      |                   ~~^~~~~~~~~~~~~
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/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o -MF CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o.d -o CMakeFiles/eludelibrary.dir/EludeCaller.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:30:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h: In constructor 'EludeCaller::EludeCaller()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:167:9: warning: 'EludeCaller::remove_non_enzymatic_' will be initialized after [-Wreorder]
  167 |    bool remove_non_enzymatic_;
      |         ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:143:9: warning:   'bool EludeCaller::context_format_' [-Wreorder]
  143 |    bool context_format_;
      |         ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:189:20: warning: 'EludeCaller::rt_model_' will be initialized after [-Wreorder]
  189 |    RetentionModel *rt_model_;
      |                    ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:173:9: warning:   'bool EludeCaller::ignore_ptms_' [-Wreorder]
  173 |    bool ignore_ptms_;
      |         ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:196:9: warning: 'EludeCaller::supress_print_' will be initialized after [-Wreorder]
  196 |    bool supress_print_;
      |         ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:175:9: warning:   'bool EludeCaller::only_hydrophobicity_index_' [-Wreorder]
  175 |    bool only_hydrophobicity_index_;
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::AddModelLibrary() const':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:519:20: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
  519 |       while (found != string::npos) {
      |              ~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::Run()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:639:9: warning: unused variable 'ret' [-Wunused-variable]
  639 |     int ret = 1;
      |         ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static double EludeCaller::ComputeRankCorrelation(std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:940:10: warning: unused variable 'corr' [-Wunused-variable]
  940 |   double corr = 0.0, d = 0.0, avg_rank, rank_p;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static std::string EludeCaller::GetFileName(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1026:39: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1026 |   if ((pos1 = path.find_last_of("/")) == string::npos) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1027:41: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1027 |     if ((pos1 = path.find_last_of("\\"))== string::npos) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1032:44: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1032 |   if ((pos2 = file_name.find_last_of(".")) != string::npos) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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/usr/bin/g++  -I/builddir/build/BUILD/percolator-rel-3-05/elude -I/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o -MF CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o.d -o CMakeFiles/eludelibrary.dir/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:21:
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC()':
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:26:1: warning:   when initialized here [-Wreorder]
   26 | PSMDescriptionDOC::PSMDescriptionDOC() :
      | ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h: In constructor 'PSMDescriptionDOC::PSMDescriptionDOC(std::string, double)':
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:42: warning: 'PSMDescriptionDOC::retentionTime_' will be initialized after [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.h:92:26: warning:   'double PSMDescriptionDOC::predictedTime_' [-Wreorder]
   92 |   double pI_, massDiff_, predictedTime_, retentionTime_;
      |                          ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/PSMDescriptionDOC.cpp:30:1: warning:   when initialized here [-Wreorder]
   30 | PSMDescriptionDOC::PSMDescriptionDOC(const string pep, const double retTime) :
      | ^~~~~~~~~~~~~~~~~
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In file included from /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:30:
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h: In constructor 'EludeCaller::EludeCaller()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:167:9: warning: 'EludeCaller::remove_non_enzymatic_' will be initialized after [-Wreorder]
  167 |    bool remove_non_enzymatic_;
      |         ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:143:9: warning:   'bool EludeCaller::context_format_' [-Wreorder]
  143 |    bool context_format_;
      |         ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:189:20: warning: 'EludeCaller::rt_model_' will be initialized after [-Wreorder]
  189 |    RetentionModel *rt_model_;
      |                    ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:173:9: warning:   'bool EludeCaller::ignore_ptms_' [-Wreorder]
  173 |    bool ignore_ptms_;
      |         ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:196:9: warning: 'EludeCaller::supress_print_' will be initialized after [-Wreorder]
  196 |    bool supress_print_;
      |         ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.h:175:9: warning:   'bool EludeCaller::only_hydrophobicity_index_' [-Wreorder]
  175 |    bool only_hydrophobicity_index_;
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:44:1: warning:   when initialized here [-Wreorder]
   44 | EludeCaller::EludeCaller():automatic_model_sel_(false), append_model_(false),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::AddModelLibrary() const':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:519:20: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
  519 |       while (found != string::npos) {
      |              ~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In member function 'int EludeCaller::Run()':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:639:9: warning: unused variable 'ret' [-Wunused-variable]
  639 |     int ret = 1;
      |         ^~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static double EludeCaller::ComputeRankCorrelation(std::vector<PSMDescription*>&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:940:10: warning: unused variable 'corr' [-Wunused-variable]
  940 |   double corr = 0.0, d = 0.0, avg_rank, rank_p;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp: In static member function 'static std::string EludeCaller::GetFileName(const std::string&)':
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1026:39: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1026 |   if ((pos1 = path.find_last_of("/")) == string::npos) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1027:41: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1027 |     if ((pos1 = path.find_last_of("\\"))== string::npos) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeCaller.cpp:1032:44: warning: comparison of integer expressions of different signedness: 'int' and 'const std::__cxx11::basic_string<char>::size_type' {aka 'const long unsigned int'} [-Wsign-compare]
 1032 |   if ((pos2 = file_name.find_last_of(".")) != string::npos) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[100%] Linking CXX executable elude
/usr/bin/cmake -E cmake_link_script CMakeFiles/elude.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -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 -Wl,-z,relro   -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 -ltirpc -rdynamic CMakeFiles/elude.dir/EludeCaller.cpp.o -o elude   -L/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/../../src  libeludelibrary.a 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[100%] Built target elude
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-05
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.94omXK
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x
++ dirname /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -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 percolator-rel-3-05
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x 'INSTALL=/usr/bin/install -p' -C percolator
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/percolator//CMakeFiles/progress.marks
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src /builddir/build/BUILD/percolator-rel-3-05/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake --color=
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-05/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake --color=
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cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/fido /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-05/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake --color=
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src /builddir/build/BUILD/percolator-rel-3-05/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake --color=
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/usr/bin/make  -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
cd /builddir/build/BUILD/percolator-rel-3-05/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05 /builddir/build/BUILD/percolator-rel-3-05/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-05/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake --color=
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make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/bin/percolator
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/bin/qvality
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x 'INSTALL=/usr/bin/install -p' -C converters
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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[ 56%] Built target converters
/usr/bin/make  -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'MSToolkit/RAMP/CMakeFiles/RAMP.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 61%] Built target RAMP
/usr/bin/make  -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'MSToolkit/CMakeFiles/MSToolkit.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 89%] Built target MSToolkit
/usr/bin/make  -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/msgf2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 92%] Built target msgf2pin
/usr/bin/make  -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/sqt2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 96%] Built target sqt2pin
/usr/bin/make  -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
cd /builddir/build/BUILD/percolator-rel-3-05/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/src/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/tandem2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/converters/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/bin/msgf2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/bin/sqt2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/bin/tandem2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/percolator/xml-1-1/mzIdentML1.1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/percolator/xml-2011.12.01.1/gaml_tandem1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/percolator/xml-2011.12.01.1/tandem2011.12.01.1.xsd
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x 'INSTALL=/usr/bin/install -p' -C elude
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool -B/builddir/build/BUILD/percolator-rel-3-05/elude --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles /builddir/build/BUILD/percolator-rel-3-05/elude//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/make  -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/eludelibrary.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/make  -f CMakeFiles/eludelibrary.dir/build.make CMakeFiles/eludelibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[2]: Nothing to be done for 'CMakeFiles/eludelibrary.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 91%] Built target eludelibrary
/usr/bin/make  -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
cd /builddir/build/BUILD/percolator-rel-3-05/elude && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles/elude.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/make  -f CMakeFiles/elude.dir/build.make CMakeFiles/elude.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[2]: Nothing to be done for 'CMakeFiles/elude.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[100%] Built target elude
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/elude/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/bin/elude
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/yeast_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/yeast_40.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/yeast_20.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/tfa.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/Luna_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/Luna_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/Luna_240.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/Luna_180.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/Luna_120.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/Jupiter_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/Jupiter_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/Jupiter_240.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/Jupiter_180.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/elude/models/Jupiter_120.model
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
+ mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/lib64/percolator
++ find . -type f '(' -name '*.a' ')'
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./elude/libeludelibrary.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libconverters.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libperclibrary_part.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/libMSToolkit.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/RAMP/libRAMP.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./fido/libfido.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/picked_protein/libpicked_protein.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/fido/libfido.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/blas/libblas.a /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/lib64/percolator
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 3.05-10.fc38 --unique-debug-suffix -3.05-10.fc38.s390x --unique-debug-src-base percolator-3.05-10.fc38.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/percolator-rel-3-05
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/bin/elude
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/bin/msgf2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/bin/percolator
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/bin/qvality
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/bin/sqt2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/bin/tandem2pin
original debug info size: 82424kB, size after compression: 66544kB
/usr/bin/sepdebugcrcfix: Updated 6 CRC32s, 0 CRC32s did match.
6052 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.s390x/src/serializer.hxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.s390x/src/serializer.cxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.s390x/src/parser.hxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.s390x/src/parser.cxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.s390x/percolator/src/Globals.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.s390x/elude/Globals.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.s390x/converters/Globals.h is executable but has no shebang, removing executable bit
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.Uf07ZL
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -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,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules'
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ LDFLAGS='-Wl,-z,relro   -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 percolator-rel-3-05
+ mkdir -p test
+ cd test
+ ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt

Pin-converter version 3.05.0, Build Date Jul 22 2022 00:00:00
Copyright (c) 2013 Lukas Käll. All rights reserved.
Written by Lukas Käll (lukas.kall@scilifelab.se) in the
School of Biotechnology at KTH - Royal Institute of Technology, Stockholm.
Issued command:
../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt
on d2e0091d3d5f4e4aa6966bd4d67856d8
Reading ../yeast-01.sqt
Reading ../yeast-01.shuffled.sqt
+ ../percolator/src/percolator -X pout.xml pin.tab
Percolator version 3.05.0, Build Date Jul 22 2022 00:00:00
Copyright (c) 2006-9 University of Washington. All rights reserved.
Written by Lukas Käll (lukall@u.washington.edu) in the
Department of Genome Sciences at the University of Washington.
Issued command:
../percolator/src/percolator -X pout.xml pin.tab
Started Mon Dec 26 12:51:40 2022
 on d2e0091d3d5f4e4aa6966bd4d67856d8
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
Reading tab-delimited input from datafile pin.tab
Features:
lnrSp deltLCn deltCn Xcorr Sp IonFrac Mass PepLen Charge1 Charge2 Charge3 enzN enzC enzInt lnNumSP dM absdM 
Found 139410 PSMs
Separate target and decoy search inputs detected, using mix-max method.
Train/test set contains 69705 positives and 69705 negatives, size ratio=1 and pi0=1
Selecting Cpos by cross-validation.
Selecting Cneg by cross-validation.
Found 7004 test set positives with q<0.01 in initial direction
Reading in data and feature calculation took 0.569989 cpu seconds or 1 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 10193 PSMs with q<0.01
Iteration 2:	Estimated 11236 PSMs with q<0.01
Iteration 3:	Estimated 11461 PSMs with q<0.01
Iteration 4:	Estimated 11509 PSMs with q<0.01
Iteration 5:	Estimated 11560 PSMs with q<0.01
Iteration 6:	Estimated 11576 PSMs with q<0.01
Iteration 7:	Estimated 11602 PSMs with q<0.01
Iteration 8:	Estimated 11617 PSMs with q<0.01
Iteration 9:	Estimated 11617 PSMs with q<0.01
Iteration 10:	Estimated 11616 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
-0.4835	-0.3200	-0.4134	lnrSp
 0.1414	 0.1989	 0.1695	deltLCn
 0.6622	 0.6394	 0.7524	deltCn
 0.6588	 0.6486	 0.6804	Xcorr
-0.0413	 0.0625	-0.0978	Sp
 0.0244	 0.1588	 0.2191	IonFrac
 0.8867	 0.6292	 0.4141	Mass
-0.7489	-0.3031	-0.0249	PepLen
 0.1083	 0.1800	 0.1009	Charge1
 0.0250	 0.0242	 0.0043	Charge2
-0.0471	-0.0610	-0.0250	Charge3
 1.3220	 1.2346	 1.2522	enzN
 1.3377	 1.1510	 1.1172	enzC
-1.9073	-1.7718	-1.6438	enzInt
-0.0159	-0.0088	 0.1201	lnNumSP
 0.0188	 0.0011	 0.0218	dM
 0.0044	 0.0139	 0.0016	absdM
-6.5792	-6.3779	-5.8394	m0
Found 11446 test set PSMs with q<0.01.
Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide.
Selecting pi_0=0.86749
Calculating q values.
New pi_0 estimate on final list yields 7371 target peptides with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 22.85 cpu seconds or 13 seconds wall clock time.
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: percolator-3.05-10.fc38.s390x
Provides: percolator = 3.05-10.fc38 percolator(s390-64) = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.2)(64bit) libc.so.6(GLIBC_2.25)(64bit) libc.so.6(GLIBC_2.28)(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_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.6)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_2.8)(64bit) libc.so.6(GLIBC_2.9)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(GOMP_4.5)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2)(64bit) libm.so.6(GLIBC_2.29)(64bit) libsqlite3.so.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(CXXABI_1.3.11)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.10)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.5)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libtirpc.so.3()(64bit) libtirpc.so.3(TIRPC_0.3.0)(64bit) libtokyocabinet.so.9()(64bit) libxerces-c-3.2.so()(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) rtld(GNU_HASH)
Obsoletes: fido-pi = 0:0
Processing files: percolator-data-3.05-10.fc38.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.1yHgeZ
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/doc/percolator-data
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/doc/percolator-data
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/doc/percolator-data
+ cp -pr src/converters/MSToolkit/RAMP/RAMP-README src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/doc/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.YCFrMw
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/licenses/percolator-data
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/licenses/percolator-data
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/licenses/percolator-data
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/licenses/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-data = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-static-3.05-10.fc38.s390x
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.xbvqw3
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/doc/percolator-static
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/doc/percolator-static
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/doc/percolator-static
+ cp -pr src/converters/MSToolkit/RAMP/RAMP-README src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/doc/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.eJb2QG
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/licenses/percolator-static
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/licenses/percolator-static
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/licenses/percolator-static
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x/usr/share/licenses/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-static = 3.05-10.fc38 percolator-static(s390-64) = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debugsource-3.05-10.fc38.s390x
Provides: percolator-debugsource = 3.05-10.fc38 percolator-debugsource(s390-64) = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debuginfo-3.05-10.fc38.s390x
Provides: debuginfo(build-id) = 0da3a8b1e8114393486ef002cb88da0622658d17 debuginfo(build-id) = 4652f624db00e5f95e432a93c19eb0be4def0c4c debuginfo(build-id) = 83435f3ae3ae1d67064d8cf322332b88ff4a3054 debuginfo(build-id) = 834a7f0f51a61a68b17e32e24486904a9febe471 debuginfo(build-id) = a62d428b95c92317555d65e153aafbc09e709432 debuginfo(build-id) = f11b6cbb0acf8bb85a53bcbe68042be4fa72965c percolator-debuginfo = 3.05-10.fc38 percolator-debuginfo(s390-64) = 3.05-10.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: percolator-debugsource(s390-64) = 3.05-10.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x
Wrote: /builddir/build/RPMS/percolator-static-3.05-10.fc38.s390x.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.05-10.fc38.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-3.05-10.fc38.s390x.rpm
Wrote: /builddir/build/RPMS/percolator-debugsource-3.05-10.fc38.s390x.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.05-10.fc38.s390x.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.EDr4sD
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/percolator-3.05-10.fc38.s390x
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.zqVRVJ
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf percolator-rel-3-05 percolator-rel-3-05.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild percolator-3.05-10.fc38.src.rpm
Finish: build phase for percolator-3.05-10.fc38.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-s390x-1672058577.895426/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-s390x-1672058577.895426/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-s390x-1672058577.895426/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/percolator-3.05-10.fc38.src.rpm) Config(child) 7 minutes 36 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool