Warning: Permanently added '3.89.133.94' (ED25519) to the list of known hosts.
Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5174200 --chroot fedora-rawhide-x86_64 --detached
Version: 0.62
PID: 105763
Logging PID: 105764
Task:
{'appstream': False,
 'background': True,
 'build_id': 5174200,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-x86_64',
 '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-x86_64/',
            '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-x86_64',
 '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-b7a9tct_/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-b7a9tct_/percolator', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-b7a9tct_/percolator'...

Running: git checkout 8a2eaf4d26f44c0df2ba49251d3666a8b439c286

cmd: ['git', 'checkout', '8a2eaf4d26f44c0df2ba49251d3666a8b439c286']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-b7a9tct_/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

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-b7a9tct_/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
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 11.5M  100 11.5M    0     0   114M      0 --:--:-- --:--:-- --:--:--  115M
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   161M      0 --:--:-- --:--:-- --:--:--  161M
INFO: Reading stdout from command: md5sum yeast-01.sqt.tar.gz

Running (timeout=115200): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-b7a9tct_/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-b7a9tct_/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1672118612.989016 -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-b7a9tct_/percolator/percolator.spec)  Config(fedora-rawhide-x86_64)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1672118612.989016/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                                 114 MB/s |  32 MB     00:00    
Additional repo https_jakub_fedorapeople_org_fe 477 kB/s |  92 kB     00:00    
fedora                                           39 MB/s |  65 MB     00:01    
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                    x86_64  1.21-1.fc38                copr_base                                        39 k
 audit-libs                      x86_64  3.0.9-2.fc38               fedora                                          116 k
 basesystem                      noarch  11-14.fc37                 fedora                                          7.0 k
 bash                            x86_64  5.2.9-3.fc38               copr_base                                       1.8 M
 bzip2-libs                      x86_64  1.0.8-12.fc38              copr_base                                        42 k
 ca-certificates                 noarch  2022.2.54-5.fc37           fedora                                          829 k
 coreutils                       x86_64  9.1-8.fc38                 copr_base                                       1.1 M
 coreutils-common                x86_64  9.1-8.fc38                 copr_base                                       2.0 M
 crypto-policies                 noarch  20221215-1.gita4c31a3.fc38 fedora                                           90 k
 curl                            x86_64  7.87.0-1.fc38              copr_base                                       346 k
 cyrus-sasl-lib                  x86_64  2.1.28-8.fc38              copr_base                                       793 k
 dbus-libs                       x86_64  1:1.14.4-1.fc38            copr_base                                       156 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                 x86_64  0.188-3.fc38               copr_base                                       196 k
 elfutils-libs                   x86_64  0.188-3.fc38               copr_base                                       257 k
 expat                           x86_64  2.5.0-1.fc38               copr_base                                       111 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                       x86_64  5.42-4.fc38                copr_base                                       676 k
 filesystem                      x86_64  3.18-2.fc37                fedora                                          1.1 M
 findutils                       x86_64  1:4.9.0-2.fc38             copr_base                                       483 k
 gawk                            x86_64  5.1.1-4.fc38               copr_base                                       1.0 M
 gdbm-libs                       x86_64  1:1.23-2.fc38              copr_base                                        56 k
 glib2                           x86_64  2.74.1-2.fc38              copr_base                                       2.7 M
 glibc                           x86_64  2.36.9000-19.fc38          fedora                                          2.1 M
 glibc-common                    x86_64  2.36.9000-19.fc38          fedora                                          309 k
 glibc-minimal-langpack          x86_64  2.36.9000-19.fc38          fedora                                           30 k
 gmp                             x86_64  1:6.2.1-3.fc38             copr_base                                       315 k
 gnupg2                          x86_64  2.3.8-1.fc38               copr_base                                       2.5 M
 gnutls                          x86_64  3.7.8-9.fc38               copr_base                                       1.1 M
 gpgme                           x86_64  1.17.1-3.fc38              copr_base                                       210 k
 grep                            x86_64  3.8-1.fc38                 copr_base                                       282 k
 ima-evm-utils                   x86_64  1.4-6.fc38                 copr_base                                        63 k
 json-c                          x86_64  0.16-3.fc38                copr_base                                        42 k
 keyutils-libs                   x86_64  1.6.1-5.fc38               copr_base                                        32 k
 krb5-libs                       x86_64  1.20.1-3.fc38              copr_base                                       719 k
 libacl                          x86_64  2.3.1-4.fc38               copr_base                                        24 k
 libarchive                      x86_64  3.6.1-3.fc38               copr_base                                       397 k
 libassuan                       x86_64  2.5.5-5.fc38               copr_base                                        68 k
 libattr                         x86_64  2.5.1-5.fc38               copr_base                                        18 k
 libb2                           x86_64  0.98.1-7.fc38              copr_base                                        25 k
 libblkid                        x86_64  2.38.1-3.fc38              fedora                                          106 k
 libbrotli                       x86_64  1.0.9-9.fc38               copr_base                                       316 k
 libcap                          x86_64  2.48-5.fc38                copr_base                                        67 k
 libcap-ng                       x86_64  0.8.3-4.fc38               copr_base                                        33 k
 libcom_err                      x86_64  1.46.5-3.fc38              copr_base                                        26 k
 libcomps                        x86_64  0.1.18-4.fc38              copr_base                                        77 k
 libcurl                         x86_64  7.87.0-1.fc38              copr_base                                       302 k
 libdnf                          x86_64  0.68.0-1.fc38              copr_base                                       659 k
 libevent                        x86_64  2.1.12-7.fc38              copr_base                                       259 k
 libffi                          x86_64  3.4.4-1.fc38               copr_base                                        38 k
 libfsverity                     x86_64  1.4-8.fc38                 copr_base                                        20 k
 libgcc                          x86_64  13.0.0-0.4.fc38            https_jakub_fedorapeople_org_fedora_gcc13_arch   93 k
 libgcrypt                       x86_64  1.10.1-6.fc38              copr_base                                       512 k
 libgomp                         x86_64  13.0.0-0.4.fc38            https_jakub_fedorapeople_org_fedora_gcc13_arch  300 k
 libgpg-error                    x86_64  1.46-1.fc38                copr_base                                       222 k
 libidn2                         x86_64  2.3.4-1.fc38               copr_base                                       154 k
 libksba                         x86_64  1.6.3-1.fc38               copr_base                                       158 k
 libmodulemd                     x86_64  2.14.0-4.fc38              copr_base                                       237 k
 libmount                        x86_64  2.38.1-3.fc38              fedora                                          135 k
 libnghttp2                      x86_64  1.51.0-1.fc38              copr_base                                        75 k
 libnsl2                         x86_64  2.0.0-4.fc38               copr_base                                        31 k
 libpsl                          x86_64  0.21.1-6.fc38              copr_base                                        65 k
 librepo                         x86_64  1.15.1-1.fc38              copr_base                                        97 k
 libreport-filesystem            noarch  2.17.6-1.fc38              copr_base                                        14 k
 libselinux                      x86_64  3.4-6.fc38                 copr_base                                        86 k
 libsemanage                     x86_64  3.4-6.fc38                 copr_base                                       120 k
 libsepol                        x86_64  3.4-4.fc38                 copr_base                                       321 k
 libsigsegv                      x86_64  2.14-3.fc38                copr_base                                        27 k
 libsmartcols                    x86_64  2.38.1-3.fc38              fedora                                           64 k
 libsolv                         x86_64  0.7.22-3.fc38              copr_base                                       406 k
 libssh                          x86_64  0.10.4-2.fc38              copr_base                                       210 k
 libssh-config                   noarch  0.10.4-2.fc38              copr_base                                       9.2 k
 libstdc++                       x86_64  13.0.0-0.4.fc38            https_jakub_fedorapeople_org_fedora_gcc13_arch  799 k
 libtasn1                        x86_64  4.19.0-1.fc38              copr_base                                        76 k
 libtirpc                        x86_64  1.3.3-0.fc38               copr_base                                        94 k
 libunistring                    x86_64  1.0-2.fc38                 copr_base                                       541 k
 libuuid                         x86_64  2.38.1-3.fc38              fedora                                           27 k
 libverto                        x86_64  0.3.2-4.fc38               copr_base                                        21 k
 libxcrypt                       x86_64  4.4.33-5.fc38              copr_base                                       120 k
 libxml2                         x86_64  2.10.3-2.fc38              copr_base                                       704 k
 libyaml                         x86_64  0.2.5-8.fc38               copr_base                                        60 k
 libzstd                         x86_64  1.5.2-3.fc37               fedora                                          294 k
 lua-libs                        x86_64  5.4.4-6.fc38               copr_base                                       133 k
 lz4-libs                        x86_64  1.9.3-5.fc38               copr_base                                        70 k
 mpdecimal                       x86_64  2.5.1-4.fc38               copr_base                                       102 k
 mpfr                            x86_64  4.1.1-2.fc38               copr_base                                       599 k
 ncurses-base                    noarch  6.3-5.20221126.fc38        copr_base                                        62 k
 ncurses-libs                    x86_64  6.3-5.20221126.fc38        copr_base                                       329 k
 nettle                          x86_64  3.8-2.fc38                 copr_base                                       414 k
 npth                            x86_64  1.6-10.fc38                copr_base                                        25 k
 openldap                        x86_64  2.6.3-1.fc38               copr_base                                       254 k
 openssl-libs                    x86_64  1:3.0.5-6.fc38             copr_base                                       2.1 M
 p11-kit                         x86_64  0.24.1-5.fc38              copr_base                                       360 k
 p11-kit-trust                   x86_64  0.24.1-5.fc38              copr_base                                       138 k
 pcre2                           x86_64  10.40-1.fc38.1             copr_base                                       236 k
 pcre2-syntax                    noarch  10.40-1.fc38.1             copr_base                                       143 k
 popt                            x86_64  1.19-1.fc38                fedora                                           66 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                         x86_64  3.11.1-1.fc38              fedora                                           27 k
 python3-dateutil                noarch  1:2.8.2-4.fc37             fedora                                          361 k
 python3-dbus                    x86_64  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                     x86_64  1.17.1-3.fc38              copr_base                                       282 k
 python3-hawkey                  x86_64  0.68.0-1.fc38              copr_base                                       110 k
 python3-libcomps                x86_64  0.1.18-4.fc38              copr_base                                        48 k
 python3-libdnf                  x86_64  0.68.0-1.fc38              copr_base                                       820 k
 python3-libs                    x86_64  3.11.1-1.fc38              fedora                                          9.6 M
 python3-rpm                     x86_64  4.18.0-8.fc38              fedora                                           94 k
 python3-six                     noarch  1.16.0-8.fc37              fedora                                           42 k
 readline                        x86_64  8.2-2.fc38                 fedora                                          211 k
 rpm                             x86_64  4.18.0-8.fc38              fedora                                          572 k
 rpm-build-libs                  x86_64  4.18.0-8.fc38              fedora                                           94 k
 rpm-libs                        x86_64  4.18.0-8.fc38              fedora                                          309 k
 rpm-sequoia                     x86_64  1.2.0-1.fc38               fedora                                          829 k
 rpm-sign-libs                   x86_64  4.18.0-8.fc38              fedora                                           27 k
 sed                             x86_64  4.8-11.fc37                fedora                                          306 k
 setup                           noarch  2.14.3-1.fc38              fedora                                          152 k
 shadow-utils                    x86_64  2:4.13-3.fc38              fedora                                          1.3 M
 sqlite-libs                     x86_64  3.40.0-1.fc38              fedora                                          661 k
 systemd-libs                    x86_64  252.4-598.fc38             fedora                                          632 k
 tpm2-tss                        x86_64  4.0.0-0.1.rc2.fc38         fedora                                          710 k
 tzdata                          noarch  2022g-1.fc38               fedora                                          716 k
 xz-libs                         x86_64  5.2.9-1.fc38               fedora                                           93 k
 zchunk-libs                     x86_64  1.2.3-1.fc38               fedora                                           51 k
 zlib                            x86_64  1.2.13-1.fc38              fedora                                           94 k

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

Total download size: 57 M
Installed size: 200 M
Downloading Packages:
(1/137): alternatives-1.21-1.fc38.x86_64.rpm    668 kB/s |  39 kB     00:00    
(2/137): bash-5.2.9-3.fc38.x86_64.rpm            28 MB/s | 1.8 MB     00:00    
(3/137): bzip2-libs-1.0.8-12.fc38.x86_64.rpm    647 kB/s |  42 kB     00:00    
(4/137): coreutils-9.1-8.fc38.x86_64.rpm        101 MB/s | 1.1 MB     00:00    
(5/137): curl-7.87.0-1.fc38.x86_64.rpm           38 MB/s | 346 kB     00:00    
(6/137): coreutils-common-9.1-8.fc38.x86_64.rpm 156 MB/s | 2.0 MB     00:00    
(7/137): cyrus-sasl-lib-2.1.28-8.fc38.x86_64.rp 116 MB/s | 793 kB     00:00    
(8/137): dbus-libs-1.14.4-1.fc38.x86_64.rpm      34 MB/s | 156 kB     00:00    
(9/137): elfutils-default-yama-scope-0.188-3.fc  15 MB/s |  16 kB     00:00    
(10/137): elfutils-libelf-0.188-3.fc38.x86_64.r  85 MB/s | 196 kB     00:00    
(11/137): elfutils-libs-0.188-3.fc38.x86_64.rpm  91 MB/s | 257 kB     00:00    
(12/137): expat-2.5.0-1.fc38.x86_64.rpm          37 MB/s | 111 kB     00:00    
(13/137): file-libs-5.42-4.fc38.x86_64.rpm      162 MB/s | 676 kB     00:00    
(14/137): findutils-4.9.0-2.fc38.x86_64.rpm      62 MB/s | 483 kB     00:00    
(15/137): gawk-5.1.1-4.fc38.x86_64.rpm          134 MB/s | 1.0 MB     00:00    
(16/137): gdbm-libs-1.23-2.fc38.x86_64.rpm       22 MB/s |  56 kB     00:00    
(17/137): gmp-6.2.1-3.fc38.x86_64.rpm           137 MB/s | 315 kB     00:00    
(18/137): gnupg2-2.3.8-1.fc38.x86_64.rpm        151 MB/s | 2.5 MB     00:00    
(19/137): glib2-2.74.1-2.fc38.x86_64.rpm        120 MB/s | 2.7 MB     00:00    
(20/137): gnutls-3.7.8-9.fc38.x86_64.rpm         49 MB/s | 1.1 MB     00:00    
(21/137): grep-3.8-1.fc38.x86_64.rpm            114 MB/s | 282 kB     00:00    
(22/137): gpgme-1.17.1-3.fc38.x86_64.rpm         21 MB/s | 210 kB     00:00    
(23/137): ima-evm-utils-1.4-6.fc38.x86_64.rpm    18 MB/s |  63 kB     00:00    
(24/137): json-c-0.16-3.fc38.x86_64.rpm          13 MB/s |  42 kB     00:00    
(25/137): keyutils-libs-1.6.1-5.fc38.x86_64.rpm  21 MB/s |  32 kB     00:00    
(26/137): krb5-libs-1.20.1-3.fc38.x86_64.rpm    237 MB/s | 719 kB     00:00    
(27/137): libacl-2.3.1-4.fc38.x86_64.rpm        6.6 MB/s |  24 kB     00:00    
(28/137): libarchive-3.6.1-3.fc38.x86_64.rpm    142 MB/s | 397 kB     00:00    
(29/137): libassuan-2.5.5-5.fc38.x86_64.rpm      40 MB/s |  68 kB     00:00    
(30/137): libattr-2.5.1-5.fc38.x86_64.rpm        18 MB/s |  18 kB     00:00    
(31/137): libbrotli-1.0.9-9.fc38.x86_64.rpm     151 MB/s | 316 kB     00:00    
(32/137): libb2-0.98.1-7.fc38.x86_64.rpm        8.5 MB/s |  25 kB     00:00    
(33/137): libcap-2.48-5.fc38.x86_64.rpm          27 MB/s |  67 kB     00:00    
(34/137): libcap-ng-0.8.3-4.fc38.x86_64.rpm      22 MB/s |  33 kB     00:00    
(35/137): libcom_err-1.46.5-3.fc38.x86_64.rpm    20 MB/s |  26 kB     00:00    
(36/137): libcurl-7.87.0-1.fc38.x86_64.rpm      149 MB/s | 302 kB     00:00    
(37/137): libcomps-0.1.18-4.fc38.x86_64.rpm      24 MB/s |  77 kB     00:00    
(38/137): libevent-2.1.12-7.fc38.x86_64.rpm      67 MB/s | 259 kB     00:00    
(39/137): libffi-3.4.4-1.fc38.x86_64.rpm        7.9 MB/s |  38 kB     00:00    
(40/137): libdnf-0.68.0-1.fc38.x86_64.rpm        76 MB/s | 659 kB     00:00    
(41/137): libfsverity-1.4-8.fc38.x86_64.rpm     9.5 MB/s |  20 kB     00:00    
(42/137): libgcrypt-1.10.1-6.fc38.x86_64.rpm    145 MB/s | 512 kB     00:00    
(43/137): libidn2-2.3.4-1.fc38.x86_64.rpm        59 MB/s | 154 kB     00:00    
(44/137): libgpg-error-1.46-1.fc38.x86_64.rpm    55 MB/s | 222 kB     00:00    
(45/137): libksba-1.6.3-1.fc38.x86_64.rpm        67 MB/s | 158 kB     00:00    
(46/137): libmodulemd-2.14.0-4.fc38.x86_64.rpm   77 MB/s | 237 kB     00:00    
(47/137): libnghttp2-1.51.0-1.fc38.x86_64.rpm    25 MB/s |  75 kB     00:00    
(48/137): libnsl2-2.0.0-4.fc38.x86_64.rpm        12 MB/s |  31 kB     00:00    
(49/137): libpsl-0.21.1-6.fc38.x86_64.rpm        22 MB/s |  65 kB     00:00    
(50/137): libreport-filesystem-2.17.6-1.fc38.no 6.0 MB/s |  14 kB     00:00    
(51/137): librepo-1.15.1-1.fc38.x86_64.rpm       28 MB/s |  97 kB     00:00    
(52/137): libselinux-3.4-6.fc38.x86_64.rpm       44 MB/s |  86 kB     00:00    
(53/137): libsemanage-3.4-6.fc38.x86_64.rpm      77 MB/s | 120 kB     00:00    
(54/137): libsepol-3.4-4.fc38.x86_64.rpm        168 MB/s | 321 kB     00:00    
(55/137): libsigsegv-2.14-3.fc38.x86_64.rpm      25 MB/s |  27 kB     00:00    
(56/137): libssh-0.10.4-2.fc38.x86_64.rpm       154 MB/s | 210 kB     00:00    
(57/137): libsolv-0.7.22-3.fc38.x86_64.rpm      111 MB/s | 406 kB     00:00    
(58/137): libssh-config-0.10.4-2.fc38.noarch.rp 3.2 MB/s | 9.2 kB     00:00    
(59/137): libtasn1-4.19.0-1.fc38.x86_64.rpm      53 MB/s |  76 kB     00:00    
(60/137): libtirpc-1.3.3-0.fc38.x86_64.rpm       80 MB/s |  94 kB     00:00    
(61/137): libunistring-1.0-2.fc38.x86_64.rpm    231 MB/s | 541 kB     00:00    
(62/137): libverto-0.3.2-4.fc38.x86_64.rpm      7.4 MB/s |  21 kB     00:00    
(63/137): libxcrypt-4.4.33-5.fc38.x86_64.rpm     42 MB/s | 120 kB     00:00    
(64/137): libxml2-2.10.3-2.fc38.x86_64.rpm      228 MB/s | 704 kB     00:00    
(65/137): lua-libs-5.4.4-6.fc38.x86_64.rpm       72 MB/s | 133 kB     00:00    
(66/137): libyaml-0.2.5-8.fc38.x86_64.rpm        17 MB/s |  60 kB     00:00    
(67/137): lz4-libs-1.9.3-5.fc38.x86_64.rpm       27 MB/s |  70 kB     00:00    
(68/137): mpfr-4.1.1-2.fc38.x86_64.rpm          222 MB/s | 599 kB     00:00    
(69/137): ncurses-base-6.3-5.20221126.fc38.noar  13 MB/s |  62 kB     00:00    
(70/137): mpdecimal-2.5.1-4.fc38.x86_64.rpm      13 MB/s | 102 kB     00:00    
(71/137): ncurses-libs-6.3-5.20221126.fc38.x86_  41 MB/s | 329 kB     00:00    
(72/137): nettle-3.8-2.fc38.x86_64.rpm           60 MB/s | 414 kB     00:00    
(73/137): openldap-2.6.3-1.fc38.x86_64.rpm      138 MB/s | 254 kB     00:00    
(74/137): npth-1.6-10.fc38.x86_64.rpm           3.0 MB/s |  25 kB     00:00    
(75/137): p11-kit-0.24.1-5.fc38.x86_64.rpm       52 MB/s | 360 kB     00:00    
(76/137): openssl-libs-3.0.5-6.fc38.x86_64.rpm  191 MB/s | 2.1 MB     00:00    
(77/137): p11-kit-trust-0.24.1-5.fc38.x86_64.rp  14 MB/s | 138 kB     00:00    
(78/137): pcre2-10.40-1.fc38.1.x86_64.rpm        59 MB/s | 236 kB     00:00    
(79/137): pcre2-syntax-10.40-1.fc38.1.noarch.rp  22 MB/s | 143 kB     00:00    
(80/137): python3-dbus-1.3.2-1.fc38.x86_64.rpm   17 MB/s | 147 kB     00:00    
(81/137): python3-gpg-1.17.1-3.fc38.x86_64.rpm   31 MB/s | 282 kB     00:00    
(82/137): python3-hawkey-0.68.0-1.fc38.x86_64.r  10 MB/s | 110 kB     00:00    
(83/137): python3-libcomps-0.1.18-4.fc38.x86_64 4.3 MB/s |  48 kB     00:00    
(84/137): python3-libdnf-0.68.0-1.fc38.x86_64.r  52 MB/s | 820 kB     00:00    
(85/137): libgcc-13.0.0-0.4.fc38.x86_64.rpm     676 kB/s |  93 kB     00:00    
(86/137): audit-libs-3.0.9-2.fc38.x86_64.rpm    4.9 MB/s | 116 kB     00:00    
(87/137): basesystem-11-14.fc37.noarch.rpm      832 kB/s | 7.0 kB     00:00    
(88/137): ca-certificates-2022.2.54-5.fc37.noar 166 MB/s | 829 kB     00:00    
(89/137): crypto-policies-20221215-1.gita4c31a3  40 MB/s |  90 kB     00:00    
(90/137): dnf-4.14.0-1.fc38.noarch.rpm          154 MB/s | 480 kB     00:00    
(91/137): dnf-data-4.14.0-1.fc38.noarch.rpm      28 MB/s |  43 kB     00:00    
(92/137): dnf-plugins-core-4.3.1-1.fc38.noarch.  31 MB/s |  34 kB     00:00    
(93/137): fedora-gpg-keys-38-0.3.noarch.rpm      63 MB/s | 125 kB     00:00    
(94/137): fedora-release-38-0.6.noarch.rpm       10 MB/s |  11 kB     00:00    
(95/137): fedora-release-common-38-0.6.noarch.r  12 MB/s |  21 kB     00:00    
(96/137): fedora-release-identity-basic-38-0.6.  11 MB/s |  11 kB     00:00    
(97/137): fedora-repos-38-0.3.noarch.rpm        9.9 MB/s |  10 kB     00:00    
(98/137): fedora-repos-rawhide-38-0.3.noarch.rp 9.5 MB/s | 9.7 kB     00:00    
(99/137): libgomp-13.0.0-0.4.fc38.x86_64.rpm    1.5 MB/s | 300 kB     00:00    
(100/137): filesystem-3.18-2.fc37.x86_64.rpm    145 MB/s | 1.1 MB     00:00    
(101/137): glibc-common-2.36.9000-19.fc38.x86_6 114 MB/s | 309 kB     00:00    
(102/137): glibc-2.36.9000-19.fc38.x86_64.rpm   239 MB/s | 2.1 MB     00:00    
(103/137): glibc-minimal-langpack-2.36.9000-19. 7.9 MB/s |  30 kB     00:00    
(104/137): libblkid-2.38.1-3.fc38.x86_64.rpm     62 MB/s | 106 kB     00:00    
(105/137): libmount-2.38.1-3.fc38.x86_64.rpm     66 MB/s | 135 kB     00:00    
(106/137): libsmartcols-2.38.1-3.fc38.x86_64.rp  33 MB/s |  64 kB     00:00    
(107/137): libuuid-2.38.1-3.fc38.x86_64.rpm      13 MB/s |  27 kB     00:00    
(108/137): libzstd-1.5.2-3.fc37.x86_64.rpm      111 MB/s | 294 kB     00:00    
(109/137): popt-1.19-1.fc38.x86_64.rpm           29 MB/s |  66 kB     00:00    
(110/137): publicsuffix-list-dafsa-20221208-1.f  39 MB/s |  59 kB     00:00    
(111/137): python-pip-wheel-22.3.1-1.fc38.noarc 206 MB/s | 1.4 MB     00:00    
(112/137): python-setuptools-wheel-65.5.1-1.fc3  88 MB/s | 715 kB     00:00    
(113/137): python3-3.11.1-1.fc38.x86_64.rpm      11 MB/s |  27 kB     00:00    
(114/137): python3-distro-1.8.0-1.fc38.noarch.r  28 MB/s |  49 kB     00:00    
(115/137): python3-dateutil-2.8.2-4.fc37.noarch  70 MB/s | 361 kB     00:00    
(116/137): python3-dnf-4.14.0-1.fc38.noarch.rpm 164 MB/s | 607 kB     00:00    
(117/137): python3-dnf-plugins-core-4.3.1-1.fc3  73 MB/s | 277 kB     00:00    
(118/137): python3-rpm-4.18.0-8.fc38.x86_64.rpm  22 MB/s |  94 kB     00:00    
(119/137): libstdc++-13.0.0-0.4.fc38.x86_64.rpm 3.4 MB/s | 799 kB     00:00    
(120/137): python3-six-1.16.0-8.fc37.noarch.rpm 1.7 MB/s |  42 kB     00:00    
(121/137): readline-8.2-2.fc38.x86_64.rpm       8.8 MB/s | 211 kB     00:00    
(122/137): rpm-4.18.0-8.fc38.x86_64.rpm          32 MB/s | 572 kB     00:00    
(123/137): rpm-build-libs-4.18.0-8.fc38.x86_64. 5.4 MB/s |  94 kB     00:00    
(124/137): rpm-libs-4.18.0-8.fc38.x86_64.rpm     79 MB/s | 309 kB     00:00    
(125/137): python3-libs-3.11.1-1.fc38.x86_64.rp 147 MB/s | 9.6 MB     00:00    
(126/137): rpm-sequoia-1.2.0-1.fc38.x86_64.rpm   51 MB/s | 829 kB     00:00    
(127/137): rpm-sign-libs-4.18.0-8.fc38.x86_64.r 2.2 MB/s |  27 kB     00:00    
(128/137): sed-4.8-11.fc37.x86_64.rpm           117 MB/s | 306 kB     00:00    
(129/137): sqlite-libs-3.40.0-1.fc38.x86_64.rpm  93 MB/s | 661 kB     00:00    
(130/137): setup-2.14.3-1.fc38.noarch.rpm        16 MB/s | 152 kB     00:00    
(131/137): shadow-utils-4.13-3.fc38.x86_64.rpm  105 MB/s | 1.3 MB     00:00    
(132/137): tpm2-tss-4.0.0-0.1.rc2.fc38.x86_64.r  96 MB/s | 710 kB     00:00    
(133/137): systemd-libs-252.4-598.fc38.x86_64.r  59 MB/s | 632 kB     00:00    
(134/137): tzdata-2022g-1.fc38.noarch.rpm        87 MB/s | 716 kB     00:00    
(135/137): xz-libs-5.2.9-1.fc38.x86_64.rpm       24 MB/s |  93 kB     00:00    
(136/137): zchunk-libs-1.2.3-1.fc38.x86_64.rpm   27 MB/s |  51 kB     00:00    
(137/137): zlib-1.2.13-1.fc38.x86_64.rpm         30 MB/s |  94 kB     00:00    
--------------------------------------------------------------------------------
Total                                            79 MB/s |  57 MB     00:00     
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.x86_64                          1/1 
  Preparing        :                                                        1/1 
  Installing       : libgcc-13.0.0-0.4.fc38.x86_64                        1/137 
  Running scriptlet: libgcc-13.0.0-0.4.fc38.x86_64                        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.x86_64                       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.x86_64             17/137 
  Running scriptlet: glibc-2.36.9000-19.fc38.x86_64                      18/137 
  Installing       : glibc-2.36.9000-19.fc38.x86_64                      18/137 
  Running scriptlet: glibc-2.36.9000-19.fc38.x86_64                      18/137 
  Installing       : bash-5.2.9-3.fc38.x86_64                            19/137 
  Running scriptlet: bash-5.2.9-3.fc38.x86_64                            19/137 
  Installing       : glibc-common-2.36.9000-19.fc38.x86_64               20/137 
  Installing       : glibc-minimal-langpack-2.36.9000-19.fc38.x86_64     21/137 
  Installing       : zlib-1.2.13-1.fc38.x86_64                           22/137 
  Installing       : bzip2-libs-1.0.8-12.fc38.x86_64                     23/137 
  Installing       : xz-libs-5.2.9-1.fc38.x86_64                         24/137 
  Installing       : libzstd-1.5.2-3.fc37.x86_64                         25/137 
  Installing       : sqlite-libs-3.40.0-1.fc38.x86_64                    26/137 
  Installing       : gmp-1:6.2.1-3.fc38.x86_64                           27/137 
  Installing       : libcap-2.48-5.fc38.x86_64                           28/137 
  Installing       : libgpg-error-1.46-1.fc38.x86_64                     29/137 
  Installing       : popt-1.19-1.fc38.x86_64                             30/137 
  Installing       : libxml2-2.10.3-2.fc38.x86_64                        31/137 
  Installing       : lua-libs-5.4.4-6.fc38.x86_64                        32/137 
  Installing       : libstdc++-13.0.0-0.4.fc38.x86_64                    33/137 
  Installing       : libuuid-2.38.1-3.fc38.x86_64                        34/137 
  Installing       : elfutils-libelf-0.188-3.fc38.x86_64                 35/137 
  Installing       : file-libs-5.42-4.fc38.x86_64                        36/137 
  Installing       : libattr-2.5.1-5.fc38.x86_64                         37/137 
  Installing       : libacl-2.3.1-4.fc38.x86_64                          38/137 
  Installing       : libffi-3.4.4-1.fc38.x86_64                          39/137 
  Installing       : p11-kit-0.24.1-5.fc38.x86_64                        40/137 
  Installing       : libunistring-1.0-2.fc38.x86_64                      41/137 
  Installing       : libidn2-2.3.4-1.fc38.x86_64                         42/137 
  Installing       : libxcrypt-4.4.33-5.fc38.x86_64                      43/137 
  Installing       : pcre2-10.40-1.fc38.1.x86_64                         44/137 
  Installing       : readline-8.2-2.fc38.x86_64                          45/137 
  Installing       : libassuan-2.5.5-5.fc38.x86_64                       46/137 
  Installing       : nettle-3.8-2.fc38.x86_64                            47/137 
  Installing       : rpm-sequoia-1.2.0-1.fc38.x86_64                     48/137 
  Installing       : expat-2.5.0-1.fc38.x86_64                           49/137 
  Installing       : gdbm-libs-1:1.23-2.fc38.x86_64                      50/137 
  Installing       : json-c-0.16-3.fc38.x86_64                           51/137 
  Installing       : keyutils-libs-1.6.1-5.fc38.x86_64                   52/137 
  Installing       : libcom_err-1.46.5-3.fc38.x86_64                     53/137 
  Installing       : libsepol-3.4-4.fc38.x86_64                          54/137 
  Installing       : libselinux-3.4-6.fc38.x86_64                        55/137 
  Installing       : sed-4.8-11.fc37.x86_64                              56/137 
  Installing       : libtasn1-4.19.0-1.fc38.x86_64                       57/137 
  Installing       : lz4-libs-1.9.3-5.fc38.x86_64                        58/137 
  Installing       : libgomp-13.0.0-0.4.fc38.x86_64                      59/137 
  Installing       : libsmartcols-2.38.1-3.fc38.x86_64                   60/137 
  Installing       : libb2-0.98.1-7.fc38.x86_64                          61/137 
  Installing       : systemd-libs-252.4-598.fc38.x86_64                  62/137 
  Installing       : dbus-libs-1:1.14.4-1.fc38.x86_64                    63/137 
  Installing       : findutils-1:4.9.0-2.fc38.x86_64                     64/137 
  Installing       : cyrus-sasl-lib-2.1.28-8.fc38.x86_64                 65/137 
  Installing       : libcomps-0.1.18-4.fc38.x86_64                       66/137 
  Installing       : grep-3.8-1.fc38.x86_64                              67/137 
  Installing       : libpsl-0.21.1-6.fc38.x86_64                         68/137 
  Installing       : libblkid-2.38.1-3.fc38.x86_64                       69/137 
  Installing       : libmount-2.38.1-3.fc38.x86_64                       70/137 
  Installing       : mpdecimal-2.5.1-4.fc38.x86_64                       71/137 
  Installing       : libgcrypt-1.10.1-6.fc38.x86_64                      72/137 
  Installing       : libksba-1.6.3-1.fc38.x86_64                         73/137 
  Installing       : mpfr-4.1.1-2.fc38.x86_64                            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.x86_64                   76/137 
  Installing       : alternatives-1.21-1.fc38.x86_64                     77/137 
  Installing       : p11-kit-trust-0.24.1-5.fc38.x86_64                  78/137 
  Running scriptlet: p11-kit-trust-0.24.1-5.fc38.x86_64                  78/137 
  Installing       : gnutls-3.7.8-9.fc38.x86_64                          79/137 
  Installing       : glib2-2.74.1-2.fc38.x86_64                          80/137 
  Installing       : libbrotli-1.0.9-9.fc38.x86_64                       81/137 
  Installing       : libcap-ng-0.8.3-4.fc38.x86_64                       82/137 
  Installing       : audit-libs-3.0.9-2.fc38.x86_64                      83/137 
  Installing       : rpm-libs-4.18.0-8.fc38.x86_64                       84/137 
  Installing       : rpm-build-libs-4.18.0-8.fc38.x86_64                 85/137 
  Installing       : libsemanage-3.4-6.fc38.x86_64                       86/137 
  Installing       : shadow-utils-2:4.13-3.fc38.x86_64                   87/137 
  Installing       : libnghttp2-1.51.0-1.fc38.x86_64                     88/137 
  Installing       : libsigsegv-2.14-3.fc38.x86_64                       89/137 
  Installing       : gawk-5.1.1-4.fc38.x86_64                            90/137 
  Installing       : libverto-0.3.2-4.fc38.x86_64                        91/137 
  Installing       : libyaml-0.2.5-8.fc38.x86_64                         92/137 
  Installing       : libmodulemd-2.14.0-4.fc38.x86_64                    93/137 
  Installing       : npth-1.6-10.fc38.x86_64                             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.x86_64                  98/137 
  Installing       : openssl-libs-1:3.0.5-6.fc38.x86_64                  99/137 
  Installing       : coreutils-9.1-8.fc38.x86_64                        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.x86_64                     102/137 
  Installing       : libtirpc-1.3.3-0.fc38.x86_64                       103/137 
  Installing       : libfsverity-1.4-8.fc38.x86_64                      104/137 
  Installing       : zchunk-libs-1.2.3-1.fc38.x86_64                    105/137 
  Installing       : libsolv-0.7.22-3.fc38.x86_64                       106/137 
  Installing       : libnsl2-2.0.0-4.fc38.x86_64                        107/137 
  Installing       : libssh-0.10.4-2.fc38.x86_64                        108/137 
  Installing       : python-pip-wheel-22.3.1-1.fc38.noarch              109/137 
  Installing       : python3-3.11.1-1.fc38.x86_64                       110/137 
  Installing       : python3-libs-3.11.1-1.fc38.x86_64                  111/137 
  Installing       : python3-dbus-1.3.2-1.fc38.x86_64                   112/137 
  Installing       : python3-libcomps-0.1.18-4.fc38.x86_64              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.x86_64                     117/137 
  Installing       : libevent-2.1.12-7.fc38.x86_64                      118/137 
  Installing       : openldap-2.6.3-1.fc38.x86_64                       119/137 
  Installing       : libcurl-7.87.0-1.fc38.x86_64                       120/137 
  Installing       : gnupg2-2.3.8-1.fc38.x86_64                         121/137 
  Installing       : gpgme-1.17.1-3.fc38.x86_64                         122/137 
  Installing       : librepo-1.15.1-1.fc38.x86_64                       123/137 
  Installing       : libdnf-0.68.0-1.fc38.x86_64                        124/137 
  Installing       : python3-libdnf-0.68.0-1.fc38.x86_64                125/137 
  Installing       : python3-hawkey-0.68.0-1.fc38.x86_64                126/137 
  Installing       : python3-gpg-1.17.1-3.fc38.x86_64                   127/137 
  Installing       : curl-7.87.0-1.fc38.x86_64                          128/137 
  Running scriptlet: tpm2-tss-4.0.0-0.1.rc2.fc38.x86_64                 129/137 
useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'

  Installing       : tpm2-tss-4.0.0-0.1.rc2.fc38.x86_64                 129/137 
  Installing       : ima-evm-utils-1.4-6.fc38.x86_64                    130/137 
  Installing       : rpm-sign-libs-4.18.0-8.fc38.x86_64                 131/137 
  Installing       : python3-rpm-4.18.0-8.fc38.x86_64                   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.x86_64                           137/137 
  Installing       : rpm-4.18.0-8.fc38.x86_64                           137/137 
  Running scriptlet: filesystem-3.18-2.fc37.x86_64                      137/137 
  Running scriptlet: ca-certificates-2022.2.54-5.fc37.noarch            137/137 
  Running scriptlet: rpm-4.18.0-8.fc38.x86_64                           137/137 
  Verifying        : alternatives-1.21-1.fc38.x86_64                      1/137 
  Verifying        : bash-5.2.9-3.fc38.x86_64                             2/137 
  Verifying        : bzip2-libs-1.0.8-12.fc38.x86_64                      3/137 
  Verifying        : coreutils-9.1-8.fc38.x86_64                          4/137 
  Verifying        : coreutils-common-9.1-8.fc38.x86_64                   5/137 
  Verifying        : curl-7.87.0-1.fc38.x86_64                            6/137 
  Verifying        : cyrus-sasl-lib-2.1.28-8.fc38.x86_64                  7/137 
  Verifying        : dbus-libs-1:1.14.4-1.fc38.x86_64                     8/137 
  Verifying        : elfutils-default-yama-scope-0.188-3.fc38.noarch      9/137 
  Verifying        : elfutils-libelf-0.188-3.fc38.x86_64                 10/137 
  Verifying        : elfutils-libs-0.188-3.fc38.x86_64                   11/137 
  Verifying        : expat-2.5.0-1.fc38.x86_64                           12/137 
  Verifying        : file-libs-5.42-4.fc38.x86_64                        13/137 
  Verifying        : findutils-1:4.9.0-2.fc38.x86_64                     14/137 
  Verifying        : gawk-5.1.1-4.fc38.x86_64                            15/137 
  Verifying        : gdbm-libs-1:1.23-2.fc38.x86_64                      16/137 
  Verifying        : glib2-2.74.1-2.fc38.x86_64                          17/137 
  Verifying        : gmp-1:6.2.1-3.fc38.x86_64                           18/137 
  Verifying        : gnupg2-2.3.8-1.fc38.x86_64                          19/137 
  Verifying        : gnutls-3.7.8-9.fc38.x86_64                          20/137 
  Verifying        : gpgme-1.17.1-3.fc38.x86_64                          21/137 
  Verifying        : grep-3.8-1.fc38.x86_64                              22/137 
  Verifying        : ima-evm-utils-1.4-6.fc38.x86_64                     23/137 
  Verifying        : json-c-0.16-3.fc38.x86_64                           24/137 
  Verifying        : keyutils-libs-1.6.1-5.fc38.x86_64                   25/137 
  Verifying        : krb5-libs-1.20.1-3.fc38.x86_64                      26/137 
  Verifying        : libacl-2.3.1-4.fc38.x86_64                          27/137 
  Verifying        : libarchive-3.6.1-3.fc38.x86_64                      28/137 
  Verifying        : libassuan-2.5.5-5.fc38.x86_64                       29/137 
  Verifying        : libattr-2.5.1-5.fc38.x86_64                         30/137 
  Verifying        : libb2-0.98.1-7.fc38.x86_64                          31/137 
  Verifying        : libbrotli-1.0.9-9.fc38.x86_64                       32/137 
  Verifying        : libcap-2.48-5.fc38.x86_64                           33/137 
  Verifying        : libcap-ng-0.8.3-4.fc38.x86_64                       34/137 
  Verifying        : libcom_err-1.46.5-3.fc38.x86_64                     35/137 
  Verifying        : libcomps-0.1.18-4.fc38.x86_64                       36/137 
  Verifying        : libcurl-7.87.0-1.fc38.x86_64                        37/137 
  Verifying        : libdnf-0.68.0-1.fc38.x86_64                         38/137 
  Verifying        : libevent-2.1.12-7.fc38.x86_64                       39/137 
  Verifying        : libffi-3.4.4-1.fc38.x86_64                          40/137 
  Verifying        : libfsverity-1.4-8.fc38.x86_64                       41/137 
  Verifying        : libgcrypt-1.10.1-6.fc38.x86_64                      42/137 
  Verifying        : libgpg-error-1.46-1.fc38.x86_64                     43/137 
  Verifying        : libidn2-2.3.4-1.fc38.x86_64                         44/137 
  Verifying        : libksba-1.6.3-1.fc38.x86_64                         45/137 
  Verifying        : libmodulemd-2.14.0-4.fc38.x86_64                    46/137 
  Verifying        : libnghttp2-1.51.0-1.fc38.x86_64                     47/137 
  Verifying        : libnsl2-2.0.0-4.fc38.x86_64                         48/137 
  Verifying        : libpsl-0.21.1-6.fc38.x86_64                         49/137 
  Verifying        : librepo-1.15.1-1.fc38.x86_64                        50/137 
  Verifying        : libreport-filesystem-2.17.6-1.fc38.noarch           51/137 
  Verifying        : libselinux-3.4-6.fc38.x86_64                        52/137 
  Verifying        : libsemanage-3.4-6.fc38.x86_64                       53/137 
  Verifying        : libsepol-3.4-4.fc38.x86_64                          54/137 
  Verifying        : libsigsegv-2.14-3.fc38.x86_64                       55/137 
  Verifying        : libsolv-0.7.22-3.fc38.x86_64                        56/137 
  Verifying        : libssh-0.10.4-2.fc38.x86_64                         57/137 
  Verifying        : libssh-config-0.10.4-2.fc38.noarch                  58/137 
  Verifying        : libtasn1-4.19.0-1.fc38.x86_64                       59/137 
  Verifying        : libtirpc-1.3.3-0.fc38.x86_64                        60/137 
  Verifying        : libunistring-1.0-2.fc38.x86_64                      61/137 
  Verifying        : libverto-0.3.2-4.fc38.x86_64                        62/137 
  Verifying        : libxcrypt-4.4.33-5.fc38.x86_64                      63/137 
  Verifying        : libxml2-2.10.3-2.fc38.x86_64                        64/137 
  Verifying        : libyaml-0.2.5-8.fc38.x86_64                         65/137 
  Verifying        : lua-libs-5.4.4-6.fc38.x86_64                        66/137 
  Verifying        : lz4-libs-1.9.3-5.fc38.x86_64                        67/137 
  Verifying        : mpdecimal-2.5.1-4.fc38.x86_64                       68/137 
  Verifying        : mpfr-4.1.1-2.fc38.x86_64                            69/137 
  Verifying        : ncurses-base-6.3-5.20221126.fc38.noarch             70/137 
  Verifying        : ncurses-libs-6.3-5.20221126.fc38.x86_64             71/137 
  Verifying        : nettle-3.8-2.fc38.x86_64                            72/137 
  Verifying        : npth-1.6-10.fc38.x86_64                             73/137 
  Verifying        : openldap-2.6.3-1.fc38.x86_64                        74/137 
  Verifying        : openssl-libs-1:3.0.5-6.fc38.x86_64                  75/137 
  Verifying        : p11-kit-0.24.1-5.fc38.x86_64                        76/137 
  Verifying        : p11-kit-trust-0.24.1-5.fc38.x86_64                  77/137 
  Verifying        : pcre2-10.40-1.fc38.1.x86_64                         78/137 
  Verifying        : pcre2-syntax-10.40-1.fc38.1.noarch                  79/137 
  Verifying        : python3-dbus-1.3.2-1.fc38.x86_64                    80/137 
  Verifying        : python3-gpg-1.17.1-3.fc38.x86_64                    81/137 
  Verifying        : python3-hawkey-0.68.0-1.fc38.x86_64                 82/137 
  Verifying        : python3-libcomps-0.1.18-4.fc38.x86_64               83/137 
  Verifying        : python3-libdnf-0.68.0-1.fc38.x86_64                 84/137 
  Verifying        : libgcc-13.0.0-0.4.fc38.x86_64                       85/137 
  Verifying        : libgomp-13.0.0-0.4.fc38.x86_64                      86/137 
  Verifying        : libstdc++-13.0.0-0.4.fc38.x86_64                    87/137 
  Verifying        : audit-libs-3.0.9-2.fc38.x86_64                      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.x86_64                      101/137 
  Verifying        : glibc-2.36.9000-19.fc38.x86_64                     102/137 
  Verifying        : glibc-common-2.36.9000-19.fc38.x86_64              103/137 
  Verifying        : glibc-minimal-langpack-2.36.9000-19.fc38.x86_64    104/137 
  Verifying        : libblkid-2.38.1-3.fc38.x86_64                      105/137 
  Verifying        : libmount-2.38.1-3.fc38.x86_64                      106/137 
  Verifying        : libsmartcols-2.38.1-3.fc38.x86_64                  107/137 
  Verifying        : libuuid-2.38.1-3.fc38.x86_64                       108/137 
  Verifying        : libzstd-1.5.2-3.fc37.x86_64                        109/137 
  Verifying        : popt-1.19-1.fc38.x86_64                            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.x86_64                       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.x86_64                  119/137 
  Verifying        : python3-rpm-4.18.0-8.fc38.x86_64                   120/137 
  Verifying        : python3-six-1.16.0-8.fc37.noarch                   121/137 
  Verifying        : readline-8.2-2.fc38.x86_64                         122/137 
  Verifying        : rpm-4.18.0-8.fc38.x86_64                           123/137 
  Verifying        : rpm-build-libs-4.18.0-8.fc38.x86_64                124/137 
  Verifying        : rpm-libs-4.18.0-8.fc38.x86_64                      125/137 
  Verifying        : rpm-sequoia-1.2.0-1.fc38.x86_64                    126/137 
  Verifying        : rpm-sign-libs-4.18.0-8.fc38.x86_64                 127/137 
  Verifying        : sed-4.8-11.fc37.x86_64                             128/137 
  Verifying        : setup-2.14.3-1.fc38.noarch                         129/137 
  Verifying        : shadow-utils-2:4.13-3.fc38.x86_64                  130/137 
  Verifying        : sqlite-libs-3.40.0-1.fc38.x86_64                   131/137 
  Verifying        : systemd-libs-252.4-598.fc38.x86_64                 132/137 
  Verifying        : tpm2-tss-4.0.0-0.1.rc2.fc38.x86_64                 133/137 
  Verifying        : tzdata-2022g-1.fc38.noarch                         134/137 
  Verifying        : xz-libs-5.2.9-1.fc38.x86_64                        135/137 
  Verifying        : zchunk-libs-1.2.3-1.fc38.x86_64                    136/137 
  Verifying        : zlib-1.2.13-1.fc38.x86_64                          137/137 
Installed products updated.

Installed:
  alternatives-1.21-1.fc38.x86_64                                               
  audit-libs-3.0.9-2.fc38.x86_64                                                
  basesystem-11-14.fc37.noarch                                                  
  bash-5.2.9-3.fc38.x86_64                                                      
  bzip2-libs-1.0.8-12.fc38.x86_64                                               
  ca-certificates-2022.2.54-5.fc37.noarch                                       
  coreutils-9.1-8.fc38.x86_64                                                   
  coreutils-common-9.1-8.fc38.x86_64                                            
  crypto-policies-20221215-1.gita4c31a3.fc38.noarch                             
  curl-7.87.0-1.fc38.x86_64                                                     
  cyrus-sasl-lib-2.1.28-8.fc38.x86_64                                           
  dbus-libs-1:1.14.4-1.fc38.x86_64                                              
  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.x86_64                                           
  elfutils-libs-0.188-3.fc38.x86_64                                             
  expat-2.5.0-1.fc38.x86_64                                                     
  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.x86_64                                                  
  filesystem-3.18-2.fc37.x86_64                                                 
  findutils-1:4.9.0-2.fc38.x86_64                                               
  gawk-5.1.1-4.fc38.x86_64                                                      
  gdbm-libs-1:1.23-2.fc38.x86_64                                                
  glib2-2.74.1-2.fc38.x86_64                                                    
  glibc-2.36.9000-19.fc38.x86_64                                                
  glibc-common-2.36.9000-19.fc38.x86_64                                         
  glibc-minimal-langpack-2.36.9000-19.fc38.x86_64                               
  gmp-1:6.2.1-3.fc38.x86_64                                                     
  gnupg2-2.3.8-1.fc38.x86_64                                                    
  gnutls-3.7.8-9.fc38.x86_64                                                    
  gpgme-1.17.1-3.fc38.x86_64                                                    
  grep-3.8-1.fc38.x86_64                                                        
  ima-evm-utils-1.4-6.fc38.x86_64                                               
  json-c-0.16-3.fc38.x86_64                                                     
  keyutils-libs-1.6.1-5.fc38.x86_64                                             
  krb5-libs-1.20.1-3.fc38.x86_64                                                
  libacl-2.3.1-4.fc38.x86_64                                                    
  libarchive-3.6.1-3.fc38.x86_64                                                
  libassuan-2.5.5-5.fc38.x86_64                                                 
  libattr-2.5.1-5.fc38.x86_64                                                   
  libb2-0.98.1-7.fc38.x86_64                                                    
  libblkid-2.38.1-3.fc38.x86_64                                                 
  libbrotli-1.0.9-9.fc38.x86_64                                                 
  libcap-2.48-5.fc38.x86_64                                                     
  libcap-ng-0.8.3-4.fc38.x86_64                                                 
  libcom_err-1.46.5-3.fc38.x86_64                                               
  libcomps-0.1.18-4.fc38.x86_64                                                 
  libcurl-7.87.0-1.fc38.x86_64                                                  
  libdnf-0.68.0-1.fc38.x86_64                                                   
  libevent-2.1.12-7.fc38.x86_64                                                 
  libffi-3.4.4-1.fc38.x86_64                                                    
  libfsverity-1.4-8.fc38.x86_64                                                 
  libgcc-13.0.0-0.4.fc38.x86_64                                                 
  libgcrypt-1.10.1-6.fc38.x86_64                                                
  libgomp-13.0.0-0.4.fc38.x86_64                                                
  libgpg-error-1.46-1.fc38.x86_64                                               
  libidn2-2.3.4-1.fc38.x86_64                                                   
  libksba-1.6.3-1.fc38.x86_64                                                   
  libmodulemd-2.14.0-4.fc38.x86_64                                              
  libmount-2.38.1-3.fc38.x86_64                                                 
  libnghttp2-1.51.0-1.fc38.x86_64                                               
  libnsl2-2.0.0-4.fc38.x86_64                                                   
  libpsl-0.21.1-6.fc38.x86_64                                                   
  librepo-1.15.1-1.fc38.x86_64                                                  
  libreport-filesystem-2.17.6-1.fc38.noarch                                     
  libselinux-3.4-6.fc38.x86_64                                                  
  libsemanage-3.4-6.fc38.x86_64                                                 
  libsepol-3.4-4.fc38.x86_64                                                    
  libsigsegv-2.14-3.fc38.x86_64                                                 
  libsmartcols-2.38.1-3.fc38.x86_64                                             
  libsolv-0.7.22-3.fc38.x86_64                                                  
  libssh-0.10.4-2.fc38.x86_64                                                   
  libssh-config-0.10.4-2.fc38.noarch                                            
  libstdc++-13.0.0-0.4.fc38.x86_64                                              
  libtasn1-4.19.0-1.fc38.x86_64                                                 
  libtirpc-1.3.3-0.fc38.x86_64                                                  
  libunistring-1.0-2.fc38.x86_64                                                
  libuuid-2.38.1-3.fc38.x86_64                                                  
  libverto-0.3.2-4.fc38.x86_64                                                  
  libxcrypt-4.4.33-5.fc38.x86_64                                                
  libxml2-2.10.3-2.fc38.x86_64                                                  
  libyaml-0.2.5-8.fc38.x86_64                                                   
  libzstd-1.5.2-3.fc37.x86_64                                                   
  lua-libs-5.4.4-6.fc38.x86_64                                                  
  lz4-libs-1.9.3-5.fc38.x86_64                                                  
  mpdecimal-2.5.1-4.fc38.x86_64                                                 
  mpfr-4.1.1-2.fc38.x86_64                                                      
  ncurses-base-6.3-5.20221126.fc38.noarch                                       
  ncurses-libs-6.3-5.20221126.fc38.x86_64                                       
  nettle-3.8-2.fc38.x86_64                                                      
  npth-1.6-10.fc38.x86_64                                                       
  openldap-2.6.3-1.fc38.x86_64                                                  
  openssl-libs-1:3.0.5-6.fc38.x86_64                                            
  p11-kit-0.24.1-5.fc38.x86_64                                                  
  p11-kit-trust-0.24.1-5.fc38.x86_64                                            
  pcre2-10.40-1.fc38.1.x86_64                                                   
  pcre2-syntax-10.40-1.fc38.1.noarch                                            
  popt-1.19-1.fc38.x86_64                                                       
  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.x86_64                                                  
  python3-dateutil-1:2.8.2-4.fc37.noarch                                        
  python3-dbus-1.3.2-1.fc38.x86_64                                              
  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.x86_64                                              
  python3-hawkey-0.68.0-1.fc38.x86_64                                           
  python3-libcomps-0.1.18-4.fc38.x86_64                                         
  python3-libdnf-0.68.0-1.fc38.x86_64                                           
  python3-libs-3.11.1-1.fc38.x86_64                                             
  python3-rpm-4.18.0-8.fc38.x86_64                                              
  python3-six-1.16.0-8.fc37.noarch                                              
  readline-8.2-2.fc38.x86_64                                                    
  rpm-4.18.0-8.fc38.x86_64                                                      
  rpm-build-libs-4.18.0-8.fc38.x86_64                                           
  rpm-libs-4.18.0-8.fc38.x86_64                                                 
  rpm-sequoia-1.2.0-1.fc38.x86_64                                               
  rpm-sign-libs-4.18.0-8.fc38.x86_64                                            
  sed-4.8-11.fc37.x86_64                                                        
  setup-2.14.3-1.fc38.noarch                                                    
  shadow-utils-2:4.13-3.fc38.x86_64                                             
  sqlite-libs-3.40.0-1.fc38.x86_64                                              
  systemd-libs-252.4-598.fc38.x86_64                                            
  tpm2-tss-4.0.0-0.1.rc2.fc38.x86_64                                            
  tzdata-2022g-1.fc38.noarch                                                    
  xz-libs-5.2.9-1.fc38.x86_64                                                   
  zchunk-libs-1.2.3-1.fc38.x86_64                                               
  zlib-1.2.13-1.fc38.x86_64                                                     

Complete!
Finish(bootstrap): dnf install
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1672118612.989016/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                                  13 kB/s | 3.0 kB     00:00    
Copr repository                                  78 MB/s |  32 MB     00:00    
Additional repo https_jakub_fedorapeople_org_fe  11 kB/s | 3.0 kB     00:00    
fedora                                          481 kB/s |  22 kB     00:00    
Dependencies resolved.
=========================================================================================================================
 Package                         Arch    Version                    Repository                                       Size
=========================================================================================================================
Installing group/module packages:
 bash                            x86_64  5.2.9-3.fc38               copr_base                                       1.8 M
 bzip2                           x86_64  1.0.8-12.fc38              copr_base                                        53 k
 coreutils                       x86_64  9.1-8.fc38                 copr_base                                       1.1 M
 cpio                            x86_64  2.13-13.fc38               copr_base                                       271 k
 diffutils                       x86_64  3.8-3.fc38                 copr_base                                       371 k
 fedora-release-common           noarch  38-0.6                     fedora                                           21 k
 findutils                       x86_64  1:4.9.0-2.fc38             copr_base                                       483 k
 gawk                            x86_64  5.1.1-4.fc38               copr_base                                       1.0 M
 glibc-minimal-langpack          x86_64  2.36.9000-19.fc38          fedora                                           30 k
 grep                            x86_64  3.8-1.fc38                 copr_base                                       282 k
 gzip                            x86_64  1.12-2.fc38                copr_base                                       159 k
 info                            x86_64  7.0.1-1.fc38               fedora                                          181 k
 patch                           x86_64  2.7.6-17.fc38              copr_base                                       125 k
 redhat-rpm-config               noarch  235-1.fc38                 fedora                                           80 k
 rpm-build                       x86_64  4.18.0-8.fc38              fedora                                           77 k
 sed                             x86_64  4.8-11.fc37                fedora                                          306 k
 shadow-utils                    x86_64  2:4.13-3.fc38              fedora                                          1.3 M
 tar                             x86_64  2:1.34-5.fc38              fedora                                          885 k
 unzip                           x86_64  6.0-58.fc38                fedora                                          182 k
 util-linux                      x86_64  2.38.1-3.fc38              fedora                                          2.3 M
 which                           x86_64  2.21-36.fc38               fedora                                           41 k
 xz                              x86_64  5.2.9-1.fc38               fedora                                          306 k
Installing dependencies:
 alternatives                    x86_64  1.21-1.fc38                copr_base                                        39 k
 ansible-srpm-macros             noarch  1-8.1.fc38                 fedora                                          8.6 k
 audit-libs                      x86_64  3.0.9-2.fc38               fedora                                          116 k
 authselect                      x86_64  1.4.2-1.fc38               copr_base                                       140 k
 authselect-libs                 x86_64  1.4.2-1.fc38               copr_base                                       237 k
 basesystem                      noarch  11-14.fc37                 fedora                                          7.0 k
 binutils                        x86_64  2.39-6.fc38                copr_base                                       5.4 M
 binutils-gold                   x86_64  2.39-6.fc38                copr_base                                       787 k
 bzip2-libs                      x86_64  1.0.8-12.fc38              copr_base                                        42 k
 ca-certificates                 noarch  2022.2.54-5.fc37           fedora                                          829 k
 coreutils-common                x86_64  9.1-8.fc38                 copr_base                                       2.0 M
 cracklib                        x86_64  2.9.7-30.fc38              copr_base                                        82 k
 crypto-policies                 noarch  20221215-1.gita4c31a3.fc38 fedora                                           90 k
 curl                            x86_64  7.87.0-1.fc38              copr_base                                       346 k
 cyrus-sasl-lib                  x86_64  2.1.28-8.fc38              copr_base                                       793 k
 debugedit                       x86_64  5.0-5.fc37                 fedora                                           77 k
 dwz                             x86_64  0.15-1.fc38                copr_base                                       137 k
 ed                              x86_64  1.18-2.fc38                copr_base                                        79 k
 efi-srpm-macros                 noarch  5-6.fc37                   fedora                                           22 k
 elfutils                        x86_64  0.188-3.fc38               copr_base                                       524 k
 elfutils-debuginfod-client      x86_64  0.188-3.fc38               copr_base                                        40 k
 elfutils-default-yama-scope     noarch  0.188-3.fc38               copr_base                                        16 k
 elfutils-libelf                 x86_64  0.188-3.fc38               copr_base                                       196 k
 elfutils-libs                   x86_64  0.188-3.fc38               copr_base                                       257 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                            x86_64  5.42-4.fc38                copr_base                                        49 k
 file-libs                       x86_64  5.42-4.fc38                copr_base                                       676 k
 filesystem                      x86_64  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                     x86_64  12.1-10.fc38               fedora                                          3.7 M
 gdbm-libs                       x86_64  1:1.23-2.fc38              copr_base                                        56 k
 ghc-srpm-macros                 noarch  1.5.0-7.fc37               fedora                                          7.8 k
 glibc                           x86_64  2.36.9000-19.fc38          fedora                                          2.1 M
 glibc-common                    x86_64  2.36.9000-19.fc38          fedora                                          309 k
 glibc-gconv-extra               x86_64  2.36.9000-19.fc38          fedora                                          1.6 M
 gmp                             x86_64  1:6.2.1-3.fc38             copr_base                                       315 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                         x86_64  2.13.1-5.fc38              copr_base                                        45 k
 kernel-srpm-macros              noarch  1.0-15.fc37                fedora                                          9.4 k
 keyutils-libs                   x86_64  1.6.1-5.fc38               copr_base                                        32 k
 krb5-libs                       x86_64  1.20.1-3.fc38              copr_base                                       719 k
 libacl                          x86_64  2.3.1-4.fc38               copr_base                                        24 k
 libarchive                      x86_64  3.6.1-3.fc38               copr_base                                       397 k
 libattr                         x86_64  2.5.1-5.fc38               copr_base                                        18 k
 libblkid                        x86_64  2.38.1-3.fc38              fedora                                          106 k
 libbrotli                       x86_64  1.0.9-9.fc38               copr_base                                       316 k
 libcap                          x86_64  2.48-5.fc38                copr_base                                        67 k
 libcap-ng                       x86_64  0.8.3-4.fc38               copr_base                                        33 k
 libcom_err                      x86_64  1.46.5-3.fc38              copr_base                                        26 k
 libcurl                         x86_64  7.87.0-1.fc38              copr_base                                       302 k
 libdb                           x86_64  5.3.28-54.fc38             copr_base                                       763 k
 libeconf                        x86_64  0.4.0-4.fc38               copr_base                                        28 k
 libevent                        x86_64  2.1.12-7.fc38              copr_base                                       259 k
 libfdisk                        x86_64  2.38.1-3.fc38              fedora                                          160 k
 libffi                          x86_64  3.4.4-1.fc38               copr_base                                        38 k
 libgcc                          x86_64  13.0.0-0.4.fc38            https_jakub_fedorapeople_org_fedora_gcc13_arch   93 k
 libgomp                         x86_64  13.0.0-0.4.fc38            https_jakub_fedorapeople_org_fedora_gcc13_arch  300 k
 libidn2                         x86_64  2.3.4-1.fc38               copr_base                                       154 k
 libmount                        x86_64  2.38.1-3.fc38              fedora                                          135 k
 libnghttp2                      x86_64  1.51.0-1.fc38              copr_base                                        75 k
 libnsl2                         x86_64  2.0.0-4.fc38               copr_base                                        31 k
 libpkgconf                      x86_64  1.8.0-3.fc37               fedora                                           36 k
 libpsl                          x86_64  0.21.1-6.fc38              copr_base                                        65 k
 libpwquality                    x86_64  1.4.5-1.fc38               fedora                                          119 k
 libselinux                      x86_64  3.4-6.fc38                 copr_base                                        86 k
 libsemanage                     x86_64  3.4-6.fc38                 copr_base                                       120 k
 libsepol                        x86_64  3.4-4.fc38                 copr_base                                       321 k
 libsigsegv                      x86_64  2.14-3.fc38                copr_base                                        27 k
 libsmartcols                    x86_64  2.38.1-3.fc38              fedora                                           64 k
 libssh                          x86_64  0.10.4-2.fc38              copr_base                                       210 k
 libssh-config                   noarch  0.10.4-2.fc38              copr_base                                       9.2 k
 libstdc++                       x86_64  13.0.0-0.4.fc38            https_jakub_fedorapeople_org_fedora_gcc13_arch  799 k
 libtasn1                        x86_64  4.19.0-1.fc38              copr_base                                        76 k
 libtirpc                        x86_64  1.3.3-0.fc38               copr_base                                        94 k
 libunistring                    x86_64  1.0-2.fc38                 copr_base                                       541 k
 libutempter                     x86_64  1.2.1-7.fc38               copr_base                                        26 k
 libuuid                         x86_64  2.38.1-3.fc38              fedora                                           27 k
 libverto                        x86_64  0.3.2-4.fc38               copr_base                                        21 k
 libxcrypt                       x86_64  4.4.33-5.fc38              copr_base                                       120 k
 libxml2                         x86_64  2.10.3-2.fc38              copr_base                                       704 k
 libzstd                         x86_64  1.5.2-3.fc37               fedora                                          294 k
 lua-libs                        x86_64  5.4.4-6.fc38               copr_base                                       133 k
 lua-srpm-macros                 noarch  1-7.fc37                   fedora                                          8.8 k
 lz4-libs                        x86_64  1.9.3-5.fc38               copr_base                                        70 k
 mpfr                            x86_64  4.1.1-2.fc38               copr_base                                       599 k
 ncurses-base                    noarch  6.3-5.20221126.fc38        copr_base                                        62 k
 ncurses-libs                    x86_64  6.3-5.20221126.fc38        copr_base                                       329 k
 nettle                          x86_64  3.8-2.fc38                 copr_base                                       414 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                        x86_64  2.6.3-1.fc38               copr_base                                       254 k
 openssl-libs                    x86_64  1:3.0.5-6.fc38             copr_base                                       2.1 M
 p11-kit                         x86_64  0.24.1-5.fc38              copr_base                                       360 k
 p11-kit-trust                   x86_64  0.24.1-5.fc38              copr_base                                       138 k
 package-notes-srpm-macros       noarch  0.5-6.fc38                 fedora                                           11 k
 pam                             x86_64  1.5.2-15.fc38              copr_base                                       521 k
 pam-libs                        x86_64  1.5.2-15.fc38              copr_base                                        57 k
 pcre2                           x86_64  10.40-1.fc38.1             copr_base                                       236 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                         x86_64  1.8.0-3.fc37               fedora                                           41 k
 pkgconf-m4                      noarch  1.8.0-3.fc37               fedora                                           14 k
 pkgconf-pkg-config              x86_64  1.8.0-3.fc37               fedora                                           10 k
 popt                            x86_64  1.19-1.fc38                fedora                                           66 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                        x86_64  8.2-2.fc38                 fedora                                          211 k
 rpm                             x86_64  4.18.0-8.fc38              fedora                                          572 k
 rpm-build-libs                  x86_64  4.18.0-8.fc38              fedora                                           94 k
 rpm-libs                        x86_64  4.18.0-8.fc38              fedora                                          309 k
 rpm-sequoia                     x86_64  1.2.0-1.fc38               fedora                                          829 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                     x86_64  3.40.0-1.fc38              fedora                                          661 k
 systemd-libs                    x86_64  252.4-598.fc38             fedora                                          632 k
 tzdata                          noarch  2022g-1.fc38               fedora                                          716 k
 util-linux-core                 x86_64  2.38.1-3.fc38              fedora                                          470 k
 xxhash-libs                     x86_64  0.8.1-3.fc37               fedora                                           41 k
 xz-libs                         x86_64  5.2.9-1.fc38               fedora                                           93 k
 zip                             x86_64  3.0-35.fc38                fedora                                          259 k
 zlib                            x86_64  1.2.13-1.fc38              fedora                                           94 k
 zstd                            x86_64  1.5.2-3.fc37               fedora                                          447 k
Installing Groups:
 Buildsystem building group                                                                                              

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

Total size: 52 M
Total download size: 379 k
Installed size: 181 M
Downloading Packages:
[SKIPPED] alternatives-1.21-1.fc38.x86_64.rpm: Already downloaded              
[SKIPPED] authselect-1.4.2-1.fc38.x86_64.rpm: Already downloaded               
[SKIPPED] authselect-libs-1.4.2-1.fc38.x86_64.rpm: Already downloaded          
[SKIPPED] bash-5.2.9-3.fc38.x86_64.rpm: Already downloaded                     
[SKIPPED] binutils-2.39-6.fc38.x86_64.rpm: Already downloaded                  
[SKIPPED] binutils-gold-2.39-6.fc38.x86_64.rpm: Already downloaded             
[SKIPPED] bzip2-1.0.8-12.fc38.x86_64.rpm: Already downloaded                   
[SKIPPED] bzip2-libs-1.0.8-12.fc38.x86_64.rpm: Already downloaded              
[SKIPPED] coreutils-9.1-8.fc38.x86_64.rpm: Already downloaded                  
[SKIPPED] coreutils-common-9.1-8.fc38.x86_64.rpm: Already downloaded           
[SKIPPED] cpio-2.13-13.fc38.x86_64.rpm: Already downloaded                     
[SKIPPED] cracklib-2.9.7-30.fc38.x86_64.rpm: Already downloaded                
[SKIPPED] curl-7.87.0-1.fc38.x86_64.rpm: Already downloaded                    
[SKIPPED] cyrus-sasl-lib-2.1.28-8.fc38.x86_64.rpm: Already downloaded          
[SKIPPED] diffutils-3.8-3.fc38.x86_64.rpm: Already downloaded                  
[SKIPPED] dwz-0.15-1.fc38.x86_64.rpm: Already downloaded                       
[SKIPPED] ed-1.18-2.fc38.x86_64.rpm: Already downloaded                        
[SKIPPED] elfutils-0.188-3.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] elfutils-debuginfod-client-0.188-3.fc38.x86_64.rpm: Already downloaded
[SKIPPED] elfutils-default-yama-scope-0.188-3.fc38.noarch.rpm: Already downloaded
[SKIPPED] elfutils-libelf-0.188-3.fc38.x86_64.rpm: Already downloaded          
[SKIPPED] elfutils-libs-0.188-3.fc38.x86_64.rpm: Already downloaded            
[SKIPPED] file-5.42-4.fc38.x86_64.rpm: Already downloaded                      
[SKIPPED] file-libs-5.42-4.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] findutils-4.9.0-2.fc38.x86_64.rpm: Already downloaded                
[SKIPPED] gawk-5.1.1-4.fc38.x86_64.rpm: Already downloaded                     
[SKIPPED] gdbm-libs-1.23-2.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] gmp-6.2.1-3.fc38.x86_64.rpm: Already downloaded                      
[SKIPPED] grep-3.8-1.fc38.x86_64.rpm: Already downloaded                       
[SKIPPED] gzip-1.12-2.fc38.x86_64.rpm: Already downloaded                      
[SKIPPED] jansson-2.13.1-5.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] keyutils-libs-1.6.1-5.fc38.x86_64.rpm: Already downloaded            
[SKIPPED] krb5-libs-1.20.1-3.fc38.x86_64.rpm: Already downloaded               
[SKIPPED] libacl-2.3.1-4.fc38.x86_64.rpm: Already downloaded                   
[SKIPPED] libarchive-3.6.1-3.fc38.x86_64.rpm: Already downloaded               
[SKIPPED] libattr-2.5.1-5.fc38.x86_64.rpm: Already downloaded                  
[SKIPPED] libbrotli-1.0.9-9.fc38.x86_64.rpm: Already downloaded                
[SKIPPED] libcap-2.48-5.fc38.x86_64.rpm: Already downloaded                    
[SKIPPED] libcap-ng-0.8.3-4.fc38.x86_64.rpm: Already downloaded                
[SKIPPED] libcom_err-1.46.5-3.fc38.x86_64.rpm: Already downloaded              
[SKIPPED] libcurl-7.87.0-1.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] libdb-5.3.28-54.fc38.x86_64.rpm: Already downloaded                  
[SKIPPED] libeconf-0.4.0-4.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] libevent-2.1.12-7.fc38.x86_64.rpm: Already downloaded                
[SKIPPED] libffi-3.4.4-1.fc38.x86_64.rpm: Already downloaded                   
[SKIPPED] libidn2-2.3.4-1.fc38.x86_64.rpm: Already downloaded                  
[SKIPPED] libnghttp2-1.51.0-1.fc38.x86_64.rpm: Already downloaded              
[SKIPPED] libnsl2-2.0.0-4.fc38.x86_64.rpm: Already downloaded                  
[SKIPPED] libpsl-0.21.1-6.fc38.x86_64.rpm: Already downloaded                  
[SKIPPED] libselinux-3.4-6.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] libsemanage-3.4-6.fc38.x86_64.rpm: Already downloaded                
[SKIPPED] libsepol-3.4-4.fc38.x86_64.rpm: Already downloaded                   
[SKIPPED] libsigsegv-2.14-3.fc38.x86_64.rpm: Already downloaded                
[SKIPPED] libssh-0.10.4-2.fc38.x86_64.rpm: Already downloaded                  
[SKIPPED] libssh-config-0.10.4-2.fc38.noarch.rpm: Already downloaded           
[SKIPPED] libtasn1-4.19.0-1.fc38.x86_64.rpm: Already downloaded                
[SKIPPED] libtirpc-1.3.3-0.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] libunistring-1.0-2.fc38.x86_64.rpm: Already downloaded               
[SKIPPED] libutempter-1.2.1-7.fc38.x86_64.rpm: Already downloaded              
[SKIPPED] libverto-0.3.2-4.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] libxcrypt-4.4.33-5.fc38.x86_64.rpm: Already downloaded               
[SKIPPED] libxml2-2.10.3-2.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] lua-libs-5.4.4-6.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] lz4-libs-1.9.3-5.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] mpfr-4.1.1-2.fc38.x86_64.rpm: Already downloaded                     
[SKIPPED] ncurses-base-6.3-5.20221126.fc38.noarch.rpm: Already downloaded      
[SKIPPED] ncurses-libs-6.3-5.20221126.fc38.x86_64.rpm: Already downloaded      
[SKIPPED] nettle-3.8-2.fc38.x86_64.rpm: Already downloaded                     
[SKIPPED] openldap-2.6.3-1.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] openssl-libs-3.0.5-6.fc38.x86_64.rpm: Already downloaded             
[SKIPPED] p11-kit-0.24.1-5.fc38.x86_64.rpm: Already downloaded                 
[SKIPPED] p11-kit-trust-0.24.1-5.fc38.x86_64.rpm: Already downloaded           
[SKIPPED] pam-1.5.2-15.fc38.x86_64.rpm: Already downloaded                     
[SKIPPED] pam-libs-1.5.2-15.fc38.x86_64.rpm: Already downloaded                
[SKIPPED] patch-2.7.6-17.fc38.x86_64.rpm: Already downloaded                   
[SKIPPED] libgcc-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded                
[SKIPPED] libgomp-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded               
[SKIPPED] libstdc++-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded             
[SKIPPED] ansible-srpm-macros-1-8.1.fc38.noarch.rpm: Already downloaded        
[SKIPPED] audit-libs-3.0.9-2.fc38.x86_64.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.x86_64.rpm: Already downloaded                  
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[SKIPPED] glibc-gconv-extra-2.36.9000-19.fc38.x86_64.rpm: Already downloaded   
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(152/153): pcre2-syntax-10.40-1.fc38.1.noarch.r 5.6 MB/s | 143 kB     00:00    
(153/153): pcre2-10.40-1.fc38.1.x86_64.rpm      8.0 MB/s | 236 kB     00:00    
--------------------------------------------------------------------------------
Total                                           3.4 MB/s | 379 kB     00:00     
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.x86_64                          1/1 
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warning: /etc/hosts created as /etc/hosts.rpmnew

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  Verifying        : coreutils-9.1-8.fc38.x86_64                          9/153 
  Verifying        : coreutils-common-9.1-8.fc38.x86_64                  10/153 
  Verifying        : cpio-2.13-13.fc38.x86_64                            11/153 
  Verifying        : cracklib-2.9.7-30.fc38.x86_64                       12/153 
  Verifying        : curl-7.87.0-1.fc38.x86_64                           13/153 
  Verifying        : cyrus-sasl-lib-2.1.28-8.fc38.x86_64                 14/153 
  Verifying        : diffutils-3.8-3.fc38.x86_64                         15/153 
  Verifying        : dwz-0.15-1.fc38.x86_64                              16/153 
  Verifying        : ed-1.18-2.fc38.x86_64                               17/153 
  Verifying        : elfutils-0.188-3.fc38.x86_64                        18/153 
  Verifying        : elfutils-debuginfod-client-0.188-3.fc38.x86_64      19/153 
  Verifying        : elfutils-default-yama-scope-0.188-3.fc38.noarch     20/153 
  Verifying        : elfutils-libelf-0.188-3.fc38.x86_64                 21/153 
  Verifying        : elfutils-libs-0.188-3.fc38.x86_64                   22/153 
  Verifying        : file-5.42-4.fc38.x86_64                             23/153 
  Verifying        : file-libs-5.42-4.fc38.x86_64                        24/153 
  Verifying        : findutils-1:4.9.0-2.fc38.x86_64                     25/153 
  Verifying        : gawk-5.1.1-4.fc38.x86_64                            26/153 
  Verifying        : gdbm-libs-1:1.23-2.fc38.x86_64                      27/153 
  Verifying        : gmp-1:6.2.1-3.fc38.x86_64                           28/153 
  Verifying        : grep-3.8-1.fc38.x86_64                              29/153 
  Verifying        : gzip-1.12-2.fc38.x86_64                             30/153 
  Verifying        : jansson-2.13.1-5.fc38.x86_64                        31/153 
  Verifying        : keyutils-libs-1.6.1-5.fc38.x86_64                   32/153 
  Verifying        : krb5-libs-1.20.1-3.fc38.x86_64                      33/153 
  Verifying        : libacl-2.3.1-4.fc38.x86_64                          34/153 
  Verifying        : libarchive-3.6.1-3.fc38.x86_64                      35/153 
  Verifying        : libattr-2.5.1-5.fc38.x86_64                         36/153 
  Verifying        : libbrotli-1.0.9-9.fc38.x86_64                       37/153 
  Verifying        : libcap-2.48-5.fc38.x86_64                           38/153 
  Verifying        : libcap-ng-0.8.3-4.fc38.x86_64                       39/153 
  Verifying        : libcom_err-1.46.5-3.fc38.x86_64                     40/153 
  Verifying        : libcurl-7.87.0-1.fc38.x86_64                        41/153 
  Verifying        : libdb-5.3.28-54.fc38.x86_64                         42/153 
  Verifying        : libeconf-0.4.0-4.fc38.x86_64                        43/153 
  Verifying        : libevent-2.1.12-7.fc38.x86_64                       44/153 
  Verifying        : libffi-3.4.4-1.fc38.x86_64                          45/153 
  Verifying        : libidn2-2.3.4-1.fc38.x86_64                         46/153 
  Verifying        : libnghttp2-1.51.0-1.fc38.x86_64                     47/153 
  Verifying        : libnsl2-2.0.0-4.fc38.x86_64                         48/153 
  Verifying        : libpsl-0.21.1-6.fc38.x86_64                         49/153 
  Verifying        : libselinux-3.4-6.fc38.x86_64                        50/153 
  Verifying        : libsemanage-3.4-6.fc38.x86_64                       51/153 
  Verifying        : libsepol-3.4-4.fc38.x86_64                          52/153 
  Verifying        : libsigsegv-2.14-3.fc38.x86_64                       53/153 
  Verifying        : libssh-0.10.4-2.fc38.x86_64                         54/153 
  Verifying        : libssh-config-0.10.4-2.fc38.noarch                  55/153 
  Verifying        : libtasn1-4.19.0-1.fc38.x86_64                       56/153 
  Verifying        : libtirpc-1.3.3-0.fc38.x86_64                        57/153 
  Verifying        : libunistring-1.0-2.fc38.x86_64                      58/153 
  Verifying        : libutempter-1.2.1-7.fc38.x86_64                     59/153 
  Verifying        : libverto-0.3.2-4.fc38.x86_64                        60/153 
  Verifying        : libxcrypt-4.4.33-5.fc38.x86_64                      61/153 
  Verifying        : libxml2-2.10.3-2.fc38.x86_64                        62/153 
  Verifying        : lua-libs-5.4.4-6.fc38.x86_64                        63/153 
  Verifying        : lz4-libs-1.9.3-5.fc38.x86_64                        64/153 
  Verifying        : mpfr-4.1.1-2.fc38.x86_64                            65/153 
  Verifying        : ncurses-base-6.3-5.20221126.fc38.noarch             66/153 
  Verifying        : ncurses-libs-6.3-5.20221126.fc38.x86_64             67/153 
  Verifying        : nettle-3.8-2.fc38.x86_64                            68/153 
  Verifying        : openldap-2.6.3-1.fc38.x86_64                        69/153 
  Verifying        : openssl-libs-1:3.0.5-6.fc38.x86_64                  70/153 
  Verifying        : p11-kit-0.24.1-5.fc38.x86_64                        71/153 
  Verifying        : p11-kit-trust-0.24.1-5.fc38.x86_64                  72/153 
  Verifying        : pam-1.5.2-15.fc38.x86_64                            73/153 
  Verifying        : pam-libs-1.5.2-15.fc38.x86_64                       74/153 
  Verifying        : patch-2.7.6-17.fc38.x86_64                          75/153 
  Verifying        : pcre2-10.40-1.fc38.1.x86_64                         76/153 
  Verifying        : pcre2-syntax-10.40-1.fc38.1.noarch                  77/153 
  Verifying        : libgcc-13.0.0-0.4.fc38.x86_64                       78/153 
  Verifying        : libgomp-13.0.0-0.4.fc38.x86_64                      79/153 
  Verifying        : libstdc++-13.0.0-0.4.fc38.x86_64                    80/153 
  Verifying        : ansible-srpm-macros-1-8.1.fc38.noarch               81/153 
  Verifying        : audit-libs-3.0.9-2.fc38.x86_64                      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.x86_64                         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.x86_64                       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.x86_64                     97/153 
  Verifying        : ghc-srpm-macros-1.5.0-7.fc37.noarch                 98/153 
  Verifying        : glibc-2.36.9000-19.fc38.x86_64                      99/153 
  Verifying        : glibc-common-2.36.9000-19.fc38.x86_64              100/153 
  Verifying        : glibc-gconv-extra-2.36.9000-19.fc38.x86_64         101/153 
  Verifying        : glibc-minimal-langpack-2.36.9000-19.fc38.x86_64    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.x86_64                           105/153 
  Verifying        : kernel-srpm-macros-1.0-15.fc37.noarch              106/153 
  Verifying        : libblkid-2.38.1-3.fc38.x86_64                      107/153 
  Verifying        : libfdisk-2.38.1-3.fc38.x86_64                      108/153 
  Verifying        : libmount-2.38.1-3.fc38.x86_64                      109/153 
  Verifying        : libpkgconf-1.8.0-3.fc37.x86_64                     110/153 
  Verifying        : libpwquality-1.4.5-1.fc38.x86_64                   111/153 
  Verifying        : libsmartcols-2.38.1-3.fc38.x86_64                  112/153 
  Verifying        : libuuid-2.38.1-3.fc38.x86_64                       113/153 
  Verifying        : libzstd-1.5.2-3.fc37.x86_64                        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.x86_64                        121/153 
  Verifying        : pkgconf-m4-1.8.0-3.fc37.noarch                     122/153 
  Verifying        : pkgconf-pkg-config-1.8.0-3.fc37.x86_64             123/153 
  Verifying        : popt-1.19-1.fc38.x86_64                            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.x86_64                         128/153 
  Verifying        : redhat-rpm-config-235-1.fc38.noarch                129/153 
  Verifying        : rpm-4.18.0-8.fc38.x86_64                           130/153 
  Verifying        : rpm-build-4.18.0-8.fc38.x86_64                     131/153 
  Verifying        : rpm-build-libs-4.18.0-8.fc38.x86_64                132/153 
  Verifying        : rpm-libs-4.18.0-8.fc38.x86_64                      133/153 
  Verifying        : rpm-sequoia-1.2.0-1.fc38.x86_64                    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.x86_64                             137/153 
  Verifying        : setup-2.14.3-1.fc38.noarch                         138/153 
  Verifying        : shadow-utils-2:4.13-3.fc38.x86_64                  139/153 
  Verifying        : sqlite-libs-3.40.0-1.fc38.x86_64                   140/153 
  Verifying        : systemd-libs-252.4-598.fc38.x86_64                 141/153 
  Verifying        : tar-2:1.34-5.fc38.x86_64                           142/153 
  Verifying        : tzdata-2022g-1.fc38.noarch                         143/153 
  Verifying        : unzip-6.0-58.fc38.x86_64                           144/153 
  Verifying        : util-linux-2.38.1-3.fc38.x86_64                    145/153 
  Verifying        : util-linux-core-2.38.1-3.fc38.x86_64               146/153 
  Verifying        : which-2.21-36.fc38.x86_64                          147/153 
  Verifying        : xxhash-libs-0.8.1-3.fc37.x86_64                    148/153 
  Verifying        : xz-5.2.9-1.fc38.x86_64                             149/153 
  Verifying        : xz-libs-5.2.9-1.fc38.x86_64                        150/153 
  Verifying        : zip-3.0-35.fc38.x86_64                             151/153 
  Verifying        : zlib-1.2.13-1.fc38.x86_64                          152/153 
  Verifying        : zstd-1.5.2-3.fc37.x86_64                           153/153 

Installed:
  alternatives-1.21-1.fc38.x86_64                                               
  ansible-srpm-macros-1-8.1.fc38.noarch                                         
  audit-libs-3.0.9-2.fc38.x86_64                                                
  authselect-1.4.2-1.fc38.x86_64                                                
  authselect-libs-1.4.2-1.fc38.x86_64                                           
  basesystem-11-14.fc37.noarch                                                  
  bash-5.2.9-3.fc38.x86_64                                                      
  binutils-2.39-6.fc38.x86_64                                                   
  binutils-gold-2.39-6.fc38.x86_64                                              
  bzip2-1.0.8-12.fc38.x86_64                                                    
  bzip2-libs-1.0.8-12.fc38.x86_64                                               
  ca-certificates-2022.2.54-5.fc37.noarch                                       
  coreutils-9.1-8.fc38.x86_64                                                   
  coreutils-common-9.1-8.fc38.x86_64                                            
  cpio-2.13-13.fc38.x86_64                                                      
  cracklib-2.9.7-30.fc38.x86_64                                                 
  crypto-policies-20221215-1.gita4c31a3.fc38.noarch                             
  curl-7.87.0-1.fc38.x86_64                                                     
  cyrus-sasl-lib-2.1.28-8.fc38.x86_64                                           
  debugedit-5.0-5.fc37.x86_64                                                   
  diffutils-3.8-3.fc38.x86_64                                                   
  dwz-0.15-1.fc38.x86_64                                                        
  ed-1.18-2.fc38.x86_64                                                         
  efi-srpm-macros-5-6.fc37.noarch                                               
  elfutils-0.188-3.fc38.x86_64                                                  
  elfutils-debuginfod-client-0.188-3.fc38.x86_64                                
  elfutils-default-yama-scope-0.188-3.fc38.noarch                               
  elfutils-libelf-0.188-3.fc38.x86_64                                           
  elfutils-libs-0.188-3.fc38.x86_64                                             
  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.x86_64                                                       
  file-libs-5.42-4.fc38.x86_64                                                  
  filesystem-3.18-2.fc37.x86_64                                                 
  findutils-1:4.9.0-2.fc38.x86_64                                               
  fonts-srpm-macros-1:2.0.5-10.fc38.noarch                                      
  fpc-srpm-macros-1.3-6.fc37.noarch                                             
  gawk-5.1.1-4.fc38.x86_64                                                      
  gdb-minimal-12.1-10.fc38.x86_64                                               
  gdbm-libs-1:1.23-2.fc38.x86_64                                                
  ghc-srpm-macros-1.5.0-7.fc37.noarch                                           
  glibc-2.36.9000-19.fc38.x86_64                                                
  glibc-common-2.36.9000-19.fc38.x86_64                                         
  glibc-gconv-extra-2.36.9000-19.fc38.x86_64                                    
  glibc-minimal-langpack-2.36.9000-19.fc38.x86_64                               
  gmp-1:6.2.1-3.fc38.x86_64                                                     
  gnat-srpm-macros-4-16.fc37.noarch                                             
  go-srpm-macros-3.2.0-1.fc38.noarch                                            
  grep-3.8-1.fc38.x86_64                                                        
  gzip-1.12-2.fc38.x86_64                                                       
  info-7.0.1-1.fc38.x86_64                                                      
  jansson-2.13.1-5.fc38.x86_64                                                  
  kernel-srpm-macros-1.0-15.fc37.noarch                                         
  keyutils-libs-1.6.1-5.fc38.x86_64                                             
  krb5-libs-1.20.1-3.fc38.x86_64                                                
  libacl-2.3.1-4.fc38.x86_64                                                    
  libarchive-3.6.1-3.fc38.x86_64                                                
  libattr-2.5.1-5.fc38.x86_64                                                   
  libblkid-2.38.1-3.fc38.x86_64                                                 
  libbrotli-1.0.9-9.fc38.x86_64                                                 
  libcap-2.48-5.fc38.x86_64                                                     
  libcap-ng-0.8.3-4.fc38.x86_64                                                 
  libcom_err-1.46.5-3.fc38.x86_64                                               
  libcurl-7.87.0-1.fc38.x86_64                                                  
  libdb-5.3.28-54.fc38.x86_64                                                   
  libeconf-0.4.0-4.fc38.x86_64                                                  
  libevent-2.1.12-7.fc38.x86_64                                                 
  libfdisk-2.38.1-3.fc38.x86_64                                                 
  libffi-3.4.4-1.fc38.x86_64                                                    
  libgcc-13.0.0-0.4.fc38.x86_64                                                 
  libgomp-13.0.0-0.4.fc38.x86_64                                                
  libidn2-2.3.4-1.fc38.x86_64                                                   
  libmount-2.38.1-3.fc38.x86_64                                                 
  libnghttp2-1.51.0-1.fc38.x86_64                                               
  libnsl2-2.0.0-4.fc38.x86_64                                                   
  libpkgconf-1.8.0-3.fc37.x86_64                                                
  libpsl-0.21.1-6.fc38.x86_64                                                   
  libpwquality-1.4.5-1.fc38.x86_64                                              
  libselinux-3.4-6.fc38.x86_64                                                  
  libsemanage-3.4-6.fc38.x86_64                                                 
  libsepol-3.4-4.fc38.x86_64                                                    
  libsigsegv-2.14-3.fc38.x86_64                                                 
  libsmartcols-2.38.1-3.fc38.x86_64                                             
  libssh-0.10.4-2.fc38.x86_64                                                   
  libssh-config-0.10.4-2.fc38.noarch                                            
  libstdc++-13.0.0-0.4.fc38.x86_64                                              
  libtasn1-4.19.0-1.fc38.x86_64                                                 
  libtirpc-1.3.3-0.fc38.x86_64                                                  
  libunistring-1.0-2.fc38.x86_64                                                
  libutempter-1.2.1-7.fc38.x86_64                                               
  libuuid-2.38.1-3.fc38.x86_64                                                  
  libverto-0.3.2-4.fc38.x86_64                                                  
  libxcrypt-4.4.33-5.fc38.x86_64                                                
  libxml2-2.10.3-2.fc38.x86_64                                                  
  libzstd-1.5.2-3.fc37.x86_64                                                   
  lua-libs-5.4.4-6.fc38.x86_64                                                  
  lua-srpm-macros-1-7.fc37.noarch                                               
  lz4-libs-1.9.3-5.fc38.x86_64                                                  
  mpfr-4.1.1-2.fc38.x86_64                                                      
  ncurses-base-6.3-5.20221126.fc38.noarch                                       
  ncurses-libs-6.3-5.20221126.fc38.x86_64                                       
  nettle-3.8-2.fc38.x86_64                                                      
  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.x86_64                                                  
  openssl-libs-1:3.0.5-6.fc38.x86_64                                            
  p11-kit-0.24.1-5.fc38.x86_64                                                  
  p11-kit-trust-0.24.1-5.fc38.x86_64                                            
  package-notes-srpm-macros-0.5-6.fc38.noarch                                   
  pam-1.5.2-15.fc38.x86_64                                                      
  pam-libs-1.5.2-15.fc38.x86_64                                                 
  patch-2.7.6-17.fc38.x86_64                                                    
  pcre2-10.40-1.fc38.1.x86_64                                                   
  pcre2-syntax-10.40-1.fc38.1.noarch                                            
  perl-srpm-macros-1-47.fc38.noarch                                             
  pkgconf-1.8.0-3.fc37.x86_64                                                   
  pkgconf-m4-1.8.0-3.fc37.noarch                                                
  pkgconf-pkg-config-1.8.0-3.fc37.x86_64                                        
  popt-1.19-1.fc38.x86_64                                                       
  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.x86_64                                                    
  redhat-rpm-config-235-1.fc38.noarch                                           
  rpm-4.18.0-8.fc38.x86_64                                                      
  rpm-build-4.18.0-8.fc38.x86_64                                                
  rpm-build-libs-4.18.0-8.fc38.x86_64                                           
  rpm-libs-4.18.0-8.fc38.x86_64                                                 
  rpm-sequoia-1.2.0-1.fc38.x86_64                                               
  rpmautospec-rpm-macros-0.3.1-1.fc38.noarch                                    
  rust-srpm-macros-23-1.fc38.noarch                                             
  sed-4.8-11.fc37.x86_64                                                        
  setup-2.14.3-1.fc38.noarch                                                    
  shadow-utils-2:4.13-3.fc38.x86_64                                             
  sqlite-libs-3.40.0-1.fc38.x86_64                                              
  systemd-libs-252.4-598.fc38.x86_64                                            
  tar-2:1.34-5.fc38.x86_64                                                      
  tzdata-2022g-1.fc38.noarch                                                    
  unzip-6.0-58.fc38.x86_64                                                      
  util-linux-2.38.1-3.fc38.x86_64                                               
  util-linux-core-2.38.1-3.fc38.x86_64                                          
  which-2.21-36.fc38.x86_64                                                     
  xxhash-libs-0.8.1-3.fc37.x86_64                                               
  xz-5.2.9-1.fc38.x86_64                                                        
  xz-libs-5.2.9-1.fc38.x86_64                                                   
  zip-3.0-35.fc38.x86_64                                                        
  zlib-1.2.13-1.fc38.x86_64                                                     
  zstd-1.5.2-3.fc37.x86_64                                                      

Complete!
Finish: dnf install
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: ghc-srpm-macros-1.5.0-7.fc37.noarch
rpm-build-4.18.0-8.fc38.x86_64
gpg-pubkey-eb10b464-6202d9c6
rpmautospec-rpm-macros-0.3.1-1.fc38.noarch
zstd-1.5.2-3.fc37.x86_64
readline-8.2-2.fc38.x86_64
libutempter-1.2.1-7.fc38.x86_64
pcre2-10.40-1.fc38.1.x86_64
file-libs-5.42-4.fc38.x86_64
libsigsegv-2.14-3.fc38.x86_64
fedora-release-identity-basic-38-0.6.noarch
libnghttp2-1.51.0-1.fc38.x86_64
rust-srpm-macros-23-1.fc38.noarch
libeconf-0.4.0-4.fc38.x86_64
libsmartcols-2.38.1-3.fc38.x86_64
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
glibc-2.36.9000-19.fc38.x86_64
dwz-0.15-1.fc38.x86_64
nettle-3.8-2.fc38.x86_64
libpwquality-1.4.5-1.fc38.x86_64
libuuid-2.38.1-3.fc38.x86_64
lz4-libs-1.9.3-5.fc38.x86_64
fedora-gpg-keys-38-0.3.noarch
libattr-2.5.1-5.fc38.x86_64
elfutils-libelf-0.188-3.fc38.x86_64
popt-1.19-1.fc38.x86_64
binutils-2.39-6.fc38.x86_64
elfutils-debuginfod-client-0.188-3.fc38.x86_64
libacl-2.3.1-4.fc38.x86_64
authselect-1.4.2-1.fc38.x86_64
sqlite-libs-3.40.0-1.fc38.x86_64
gdb-minimal-12.1-10.fc38.x86_64
zip-3.0-35.fc38.x86_64
ncurses-base-6.3-5.20221126.fc38.noarch
libcom_err-1.46.5-3.fc38.x86_64
gdbm-libs-1.23-2.fc38.x86_64
libselinux-3.4-6.fc38.x86_64
libnsl2-2.0.0-4.fc38.x86_64
pkgconf-m4-1.8.0-3.fc37.noarch
sed-4.8-11.fc37.x86_64
cpio-2.13-13.fc38.x86_64
libdb-5.3.28-54.fc38.x86_64
grep-3.8-1.fc38.x86_64
libblkid-2.38.1-3.fc38.x86_64
gpg-pubkey-5323552a-6112bcdc
glibc-gconv-extra-2.36.9000-19.fc38.x86_64
go-srpm-macros-3.2.0-1.fc38.noarch
elfutils-default-yama-scope-0.188-3.fc38.noarch
gmp-6.2.1-3.fc38.x86_64
libunistring-1.0-2.fc38.x86_64
openssl-libs-3.0.5-6.fc38.x86_64
efi-srpm-macros-5-6.fc37.noarch
openblas-srpm-macros-2-12.fc37.noarch
fpc-srpm-macros-1.3-6.fc37.noarch
shadow-utils-4.13-3.fc38.x86_64
util-linux-2.38.1-3.fc38.x86_64
zlib-1.2.13-1.fc38.x86_64
findutils-4.9.0-2.fc38.x86_64
unzip-6.0-58.fc38.x86_64
libgomp-13.0.0-0.4.fc38.x86_64
libbrotli-1.0.9-9.fc38.x86_64
libffi-3.4.4-1.fc38.x86_64
ca-certificates-2022.2.54-5.fc37.noarch
ed-1.18-2.fc38.x86_64
libssh-0.10.4-2.fc38.x86_64
qt5-srpm-macros-5.15.7-1.fc38.noarch
libgcc-13.0.0-0.4.fc38.x86_64
libzstd-1.5.2-3.fc37.x86_64
curl-7.87.0-1.fc38.x86_64
glibc-minimal-langpack-2.36.9000-19.fc38.x86_64
libcap-2.48-5.fc38.x86_64
p11-kit-trust-0.24.1-5.fc38.x86_64
authselect-libs-1.4.2-1.fc38.x86_64
lua-srpm-macros-1-7.fc37.noarch
jansson-2.13.1-5.fc38.x86_64
lua-libs-5.4.4-6.fc38.x86_64
coreutils-9.1-8.fc38.x86_64
rpm-sequoia-1.2.0-1.fc38.x86_64
systemd-libs-252.4-598.fc38.x86_64
krb5-libs-1.20.1-3.fc38.x86_64
file-5.42-4.fc38.x86_64
pkgconf-1.8.0-3.fc37.x86_64
libarchive-3.6.1-3.fc38.x86_64
libfdisk-2.38.1-3.fc38.x86_64
rpm-build-libs-4.18.0-8.fc38.x86_64
cracklib-2.9.7-30.fc38.x86_64
mpfr-4.1.1-2.fc38.x86_64
libmount-2.38.1-3.fc38.x86_64
keyutils-libs-1.6.1-5.fc38.x86_64
p11-kit-0.24.1-5.fc38.x86_64
libpkgconf-1.8.0-3.fc37.x86_64
python-srpm-macros-3.11-6.fc38.noarch
info-7.0.1-1.fc38.x86_64
elfutils-libs-0.188-3.fc38.x86_64
kernel-srpm-macros-1.0-15.fc37.noarch
gzip-1.12-2.fc38.x86_64
xz-5.2.9-1.fc38.x86_64
which-2.21-36.fc38.x86_64
libverto-0.3.2-4.fc38.x86_64
fonts-srpm-macros-2.0.5-10.fc38.noarch
pam-libs-1.5.2-15.fc38.x86_64
libxml2-2.10.3-2.fc38.x86_64
ncurses-libs-6.3-5.20221126.fc38.x86_64
rpm-libs-4.18.0-8.fc38.x86_64
fedora-release-common-38-0.6.noarch
util-linux-core-2.38.1-3.fc38.x86_64
perl-srpm-macros-1-47.fc38.noarch
ansible-srpm-macros-1-8.1.fc38.noarch
alternatives-1.21-1.fc38.x86_64
cyrus-sasl-lib-2.1.28-8.fc38.x86_64
pkgconf-pkg-config-1.8.0-3.fc37.x86_64
glibc-common-2.36.9000-19.fc38.x86_64
audit-libs-3.0.9-2.fc38.x86_64
fedora-repos-rawhide-38-0.3.noarch
package-notes-srpm-macros-0.5-6.fc38.noarch
redhat-rpm-config-235-1.fc38.noarch
publicsuffix-list-dafsa-20221208-1.fc38.noarch
libxcrypt-4.4.33-5.fc38.x86_64
patch-2.7.6-17.fc38.x86_64
fedora-release-38-0.6.noarch
debugedit-5.0-5.fc37.x86_64
filesystem-3.18-2.fc37.x86_64
tzdata-2022g-1.fc38.noarch
elfutils-0.188-3.fc38.x86_64
gawk-5.1.1-4.fc38.x86_64
libsemanage-3.4-6.fc38.x86_64
diffutils-3.8-3.fc38.x86_64
libpsl-0.21.1-6.fc38.x86_64
libidn2-2.3.4-1.fc38.x86_64
libtasn1-4.19.0-1.fc38.x86_64
libtirpc-1.3.3-0.fc38.x86_64
pam-1.5.2-15.fc38.x86_64
libcap-ng-0.8.3-4.fc38.x86_64
nim-srpm-macros-3-7.fc37.noarch
libcurl-7.87.0-1.fc38.x86_64
xz-libs-5.2.9-1.fc38.x86_64
bzip2-1.0.8-12.fc38.x86_64
setup-2.14.3-1.fc38.noarch
binutils-gold-2.39-6.fc38.x86_64
coreutils-common-9.1-8.fc38.x86_64
ocaml-srpm-macros-7-2.fc37.noarch
libstdc++-13.0.0-0.4.fc38.x86_64
bash-5.2.9-3.fc38.x86_64
openldap-2.6.3-1.fc38.x86_64
libsepol-3.4-4.fc38.x86_64
fedora-repos-38-0.3.noarch
bzip2-libs-1.0.8-12.fc38.x86_64
libssh-config-0.10.4-2.fc38.noarch
libevent-2.1.12-7.fc38.x86_64
tar-1.34-5.fc38.x86_64
pcre2-syntax-10.40-1.fc38.1.noarch
rpm-4.18.0-8.fc38.x86_64
gnat-srpm-macros-4-16.fc37.noarch
xxhash-libs-0.8.1-3.fc37.x86_64
basesystem-11-14.fc37.noarch
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: x86_64
Building for target x86_64
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-x86_64-1672118612.989016/root/var/log’: No such file or directory
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1672118612.989016/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-x86_64-1672118612.989016/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-x86_64-1672118612.989016/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-b7a9tct_/percolator/percolator.spec) Config(child) 0 minutes 56 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
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 1672118612.989016 -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-x86_64)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1672118612.989016/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1672118612.989016/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1672118612.989016/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                                  48 kB/s | 3.0 kB     00:00    
Additional repo https_jakub_fedorapeople_org_fe  12 kB/s | 3.0 kB     00:00    
fedora                                           50 kB/s |  22 kB     00:00    
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: x86_64
Building for target x86_64
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                                  13 kB/s | 3.0 kB     00:00    
Additional repo https_jakub_fedorapeople_org_fe  11 kB/s | 3.0 kB     00:00    
fedora                                           94 kB/s |  22 kB     00:00    
Dependencies resolved.
==============================================================================================================
 Package                     Arch    Version             Repository                                       Size
==============================================================================================================
Installing:
 boost-devel                 x86_64  1.78.0-9.fc38       copr_base                                        11 M
 boost-static                x86_64  1.78.0-9.fc38       copr_base                                       3.6 M
 bzip2-devel                 x86_64  1.0.8-12.fc38       copr_base                                       214 k
 cmake                       x86_64  3.25.1-1.fc38       copr_base                                       7.0 M
 gcc                         x86_64  13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch   34 M
 gcc-c++                     x86_64  13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch   13 M
 libtirpc-devel              x86_64  1.3.3-0.fc38        copr_base                                       113 k
 make                        x86_64  1:4.3-11.fc38       copr_base                                       534 k
 sqlite-devel                x86_64  3.40.0-1.fc38       fedora                                          143 k
 tokyocabinet-devel          x86_64  1.4.48-20.fc37      fedora                                           93 k
 xerces-c-devel              x86_64  3.2.3-7.fc37        fedora                                          509 k
 xsd                         x86_64  4.1.0-0.10.a11.fc37 fedora                                          1.2 M
 zlib-devel                  x86_64  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          x86_64  10.99-1.0.1.fc38    https_jakub_fedorapeople_org_fedora_gcc13_arch  889 k
 boost                       x86_64  1.78.0-9.fc38       copr_base                                        15 k
 boost-atomic                x86_64  1.78.0-9.fc38       copr_base                                        21 k
 boost-chrono                x86_64  1.78.0-9.fc38       copr_base                                        27 k
 boost-container             x86_64  1.78.0-9.fc38       copr_base                                        41 k
 boost-context               x86_64  1.78.0-9.fc38       copr_base                                        18 k
 boost-contract              x86_64  1.78.0-9.fc38       copr_base                                        48 k
 boost-coroutine             x86_64  1.78.0-9.fc38       copr_base                                        23 k
 boost-date-time             x86_64  1.78.0-9.fc38       copr_base                                        17 k
 boost-fiber                 x86_64  1.78.0-9.fc38       copr_base                                        43 k
 boost-filesystem            x86_64  1.78.0-9.fc38       copr_base                                        67 k
 boost-graph                 x86_64  1.78.0-9.fc38       copr_base                                       151 k
 boost-iostreams             x86_64  1.78.0-9.fc38       copr_base                                        43 k
 boost-json                  x86_64  1.78.0-9.fc38       copr_base                                       112 k
 boost-locale                x86_64  1.78.0-9.fc38       copr_base                                       223 k
 boost-log                   x86_64  1.78.0-9.fc38       copr_base                                       493 k
 boost-math                  x86_64  1.78.0-9.fc38       copr_base                                       204 k
 boost-nowide                x86_64  1.78.0-9.fc38       copr_base                                        22 k
 boost-numpy3                x86_64  1.78.0-9.fc38       copr_base                                        30 k
 boost-program-options       x86_64  1.78.0-9.fc38       copr_base                                       110 k
 boost-python3               x86_64  1.78.0-9.fc38       copr_base                                        97 k
 boost-random                x86_64  1.78.0-9.fc38       copr_base                                        26 k
 boost-regex                 x86_64  1.78.0-9.fc38       copr_base                                       113 k
 boost-serialization         x86_64  1.78.0-9.fc38       copr_base                                       135 k
 boost-stacktrace            x86_64  1.78.0-9.fc38       copr_base                                        31 k
 boost-system                x86_64  1.78.0-9.fc38       copr_base                                        17 k
 boost-test                  x86_64  1.78.0-9.fc38       copr_base                                       240 k
 boost-thread                x86_64  1.78.0-9.fc38       copr_base                                        60 k
 boost-timer                 x86_64  1.78.0-9.fc38       copr_base                                        26 k
 boost-type_erasure          x86_64  1.78.0-9.fc38       copr_base                                        35 k
 boost-wave                  x86_64  1.78.0-9.fc38       copr_base                                       221 k
 cmake-data                  noarch  3.25.1-1.fc38       copr_base                                       1.7 M
 cmake-filesystem            x86_64  3.25.1-1.fc38       copr_base                                        17 k
 cmake-rpm-macros            noarch  3.25.1-1.fc38       copr_base                                        16 k
 cpp                         x86_64  13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch   11 M
 emacs-filesystem            noarch  1:28.1-3.fc37       fedora                                          9.5 k
 expat                       x86_64  2.5.0-1.fc38        copr_base                                       111 k
 flexiblas                   x86_64  3.2.1-3.fc38        fedora                                           32 k
 flexiblas-netlib            x86_64  3.2.1-3.fc38        fedora                                          3.1 M
 flexiblas-openblas-openmp   x86_64  3.2.1-3.fc38        fedora                                           17 k
 gc                          x86_64  8.2.2-1.fc38        copr_base                                       111 k
 gcc-plugin-annobin          x86_64  13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch   29 k
 glibc-devel                 x86_64  2.36.9000-19.fc38   fedora                                           47 k
 glibc-headers-x86           noarch  2.36.9000-19.fc38   fedora                                          525 k
 guile22                     x86_64  2.2.7-6.fc38        copr_base                                       6.4 M
 jsoncpp                     x86_64  1.9.5-3.fc38        copr_base                                        98 k
 kernel-headers              x86_64  6.1.0-1.fc38        fedora                                          1.5 M
 libb2                       x86_64  0.98.1-7.fc38       copr_base                                        25 k
 libcutl                     x86_64  1.10.0-25.fc38      copr_base                                       315 k
 libgfortran                 x86_64  13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch  890 k
 libicu                      x86_64  71.1-2.fc38         copr_base                                        10 M
 libicu-devel                x86_64  71.1-2.fc38         copr_base                                       842 k
 libmpc                      x86_64  1.2.1-5.fc38        copr_base                                        61 k
 libquadmath                 x86_64  13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch  178 k
 libquadmath-devel           x86_64  13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch   20 k
 libstdc++-devel             x86_64  13.0.0-0.4.fc38     https_jakub_fedorapeople_org_fedora_gcc13_arch  2.4 M
 libtool-ltdl                x86_64  2.4.7-3.0.1.fc38    https_jakub_fedorapeople_org_fedora_gcc13_arch   37 k
 libuv                       x86_64  1:1.44.2-2.fc38     copr_base                                       152 k
 libxcrypt-devel             x86_64  4.4.33-5.fc38       copr_base                                        31 k
 mpdecimal                   x86_64  2.5.1-4.fc38        copr_base                                       102 k
 openblas                    x86_64  0.3.21-4.fc38       fedora                                           35 k
 openblas-openmp             x86_64  0.3.21-4.fc38       fedora                                          5.1 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                     x86_64  3.11.1-1.fc38       fedora                                           27 k
 python3-libs                x86_64  3.11.1-1.fc38       fedora                                          9.6 M
 python3-numpy               x86_64  1:1.23.5-1.fc38     copr_base                                       7.3 M
 rhash                       x86_64  1.4.3-1.fc38        fedora                                          193 k
 sqlite                      x86_64  3.40.0-1.fc38       fedora                                          811 k
 tokyocabinet                x86_64  1.4.48-20.fc37      fedora                                          514 k
 vim-filesystem              noarch  2:9.0.1054-1.fc38   fedora                                           19 k
 xerces-c                    x86_64  3.2.3-7.fc37        fedora                                          960 k

Transaction Summary
==============================================================================================================
Install  86 Packages

Total size: 141 M
Total download size: 59 M
Installed size: 657 M
Downloading Packages:
[SKIPPED] cmake-filesystem-3.25.1-1.fc38.x86_64.rpm: Already downloaded        
[SKIPPED] expat-2.5.0-1.fc38.x86_64.rpm: Already downloaded                    
[SKIPPED] gc-8.2.2-1.fc38.x86_64.rpm: Already downloaded                       
[SKIPPED] guile22-2.2.7-6.fc38.x86_64.rpm: Already downloaded                  
[SKIPPED] libb2-0.98.1-7.fc38.x86_64.rpm: Already downloaded                   
[SKIPPED] libmpc-1.2.1-5.fc38.x86_64.rpm: Already downloaded                   
[SKIPPED] libxcrypt-devel-4.4.33-5.fc38.x86_64.rpm: Already downloaded         
[SKIPPED] make-4.3-11.fc38.x86_64.rpm: Already downloaded                      
[SKIPPED] mpdecimal-2.5.1-4.fc38.x86_64.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.x86_64.rpm: Already downloaded   
[SKIPPED] cpp-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded                   
[SKIPPED] gcc-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded                   
[SKIPPED] gcc-c++-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded               
[SKIPPED] gcc-plugin-annobin-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded    
[SKIPPED] libstdc++-devel-13.0.0-0.4.fc38.x86_64.rpm: Already downloaded       
[SKIPPED] libtool-ltdl-2.4.7-3.0.1.fc38.x86_64.rpm: Already downloaded         
[SKIPPED] emacs-filesystem-28.1-3.fc37.noarch.rpm: Already downloaded          
[SKIPPED] glibc-devel-2.36.9000-19.fc38.x86_64.rpm: Already downloaded         
[SKIPPED] glibc-headers-x86-2.36.9000-19.fc38.noarch.rpm: Already downloaded   
[SKIPPED] kernel-headers-6.1.0-1.fc38.x86_64.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.x86_64.rpm: Already downloaded                 
[SKIPPED] python3-libs-3.11.1-1.fc38.x86_64.rpm: Already downloaded            
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Total                                            61 MB/s |  59 MB     00:00     
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  Verifying        : vim-filesystem-2:9.0.1054-1.fc38.noarch              82/86 
  Verifying        : xerces-c-3.2.3-7.fc37.x86_64                         83/86 
  Verifying        : xerces-c-devel-3.2.3-7.fc37.x86_64                   84/86 
  Verifying        : xsd-4.1.0-0.10.a11.fc37.x86_64                       85/86 
  Verifying        : zlib-devel-1.2.13-1.fc38.x86_64                      86/86 

Installed:
  annobin-docs-10.99-1.0.1.fc38.noarch                                          
  annobin-plugin-gcc-10.99-1.0.1.fc38.x86_64                                    
  boost-1.78.0-9.fc38.x86_64                                                    
  boost-atomic-1.78.0-9.fc38.x86_64                                             
  boost-chrono-1.78.0-9.fc38.x86_64                                             
  boost-container-1.78.0-9.fc38.x86_64                                          
  boost-context-1.78.0-9.fc38.x86_64                                            
  boost-contract-1.78.0-9.fc38.x86_64                                           
  boost-coroutine-1.78.0-9.fc38.x86_64                                          
  boost-date-time-1.78.0-9.fc38.x86_64                                          
  boost-devel-1.78.0-9.fc38.x86_64                                              
  boost-fiber-1.78.0-9.fc38.x86_64                                              
  boost-filesystem-1.78.0-9.fc38.x86_64                                         
  boost-graph-1.78.0-9.fc38.x86_64                                              
  boost-iostreams-1.78.0-9.fc38.x86_64                                          
  boost-json-1.78.0-9.fc38.x86_64                                               
  boost-locale-1.78.0-9.fc38.x86_64                                             
  boost-log-1.78.0-9.fc38.x86_64                                                
  boost-math-1.78.0-9.fc38.x86_64                                               
  boost-nowide-1.78.0-9.fc38.x86_64                                             
  boost-numpy3-1.78.0-9.fc38.x86_64                                             
  boost-program-options-1.78.0-9.fc38.x86_64                                    
  boost-python3-1.78.0-9.fc38.x86_64                                            
  boost-random-1.78.0-9.fc38.x86_64                                             
  boost-regex-1.78.0-9.fc38.x86_64                                              
  boost-serialization-1.78.0-9.fc38.x86_64                                      
  boost-stacktrace-1.78.0-9.fc38.x86_64                                         
  boost-static-1.78.0-9.fc38.x86_64                                             
  boost-system-1.78.0-9.fc38.x86_64                                             
  boost-test-1.78.0-9.fc38.x86_64                                               
  boost-thread-1.78.0-9.fc38.x86_64                                             
  boost-timer-1.78.0-9.fc38.x86_64                                              
  boost-type_erasure-1.78.0-9.fc38.x86_64                                       
  boost-wave-1.78.0-9.fc38.x86_64                                               
  bzip2-devel-1.0.8-12.fc38.x86_64                                              
  cmake-3.25.1-1.fc38.x86_64                                                    
  cmake-data-3.25.1-1.fc38.noarch                                               
  cmake-filesystem-3.25.1-1.fc38.x86_64                                         
  cmake-rpm-macros-3.25.1-1.fc38.noarch                                         
  cpp-13.0.0-0.4.fc38.x86_64                                                    
  emacs-filesystem-1:28.1-3.fc37.noarch                                         
  expat-2.5.0-1.fc38.x86_64                                                     
  flexiblas-3.2.1-3.fc38.x86_64                                                 
  flexiblas-netlib-3.2.1-3.fc38.x86_64                                          
  flexiblas-openblas-openmp-3.2.1-3.fc38.x86_64                                 
  gc-8.2.2-1.fc38.x86_64                                                        
  gcc-13.0.0-0.4.fc38.x86_64                                                    
  gcc-c++-13.0.0-0.4.fc38.x86_64                                                
  gcc-plugin-annobin-13.0.0-0.4.fc38.x86_64                                     
  glibc-devel-2.36.9000-19.fc38.x86_64                                          
  glibc-headers-x86-2.36.9000-19.fc38.noarch                                    
  guile22-2.2.7-6.fc38.x86_64                                                   
  jsoncpp-1.9.5-3.fc38.x86_64                                                   
  kernel-headers-6.1.0-1.fc38.x86_64                                            
  libb2-0.98.1-7.fc38.x86_64                                                    
  libcutl-1.10.0-25.fc38.x86_64                                                 
  libgfortran-13.0.0-0.4.fc38.x86_64                                            
  libicu-71.1-2.fc38.x86_64                                                     
  libicu-devel-71.1-2.fc38.x86_64                                               
  libmpc-1.2.1-5.fc38.x86_64                                                    
  libquadmath-13.0.0-0.4.fc38.x86_64                                            
  libquadmath-devel-13.0.0-0.4.fc38.x86_64                                      
  libstdc++-devel-13.0.0-0.4.fc38.x86_64                                        
  libtirpc-devel-1.3.3-0.fc38.x86_64                                            
  libtool-ltdl-2.4.7-3.0.1.fc38.x86_64                                          
  libuv-1:1.44.2-2.fc38.x86_64                                                  
  libxcrypt-devel-4.4.33-5.fc38.x86_64                                          
  make-1:4.3-11.fc38.x86_64                                                     
  mpdecimal-2.5.1-4.fc38.x86_64                                                 
  openblas-0.3.21-4.fc38.x86_64                                                 
  openblas-openmp-0.3.21-4.fc38.x86_64                                          
  python-pip-wheel-22.3.1-1.fc38.noarch                                         
  python-setuptools-wheel-65.5.1-1.fc38.noarch                                  
  python3-3.11.1-1.fc38.x86_64                                                  
  python3-libs-3.11.1-1.fc38.x86_64                                             
  python3-numpy-1:1.23.5-1.fc38.x86_64                                          
  rhash-1.4.3-1.fc38.x86_64                                                     
  sqlite-3.40.0-1.fc38.x86_64                                                   
  sqlite-devel-3.40.0-1.fc38.x86_64                                             
  tokyocabinet-1.4.48-20.fc37.x86_64                                            
  tokyocabinet-devel-1.4.48-20.fc37.x86_64                                      
  vim-filesystem-2:9.0.1054-1.fc38.noarch                                       
  xerces-c-3.2.3-7.fc37.x86_64                                                  
  xerces-c-devel-3.2.3-7.fc37.x86_64                                            
  xsd-4.1.0-0.10.a11.fc37.x86_64                                                
  zlib-devel-1.2.13-1.fc38.x86_64                                               

Complete!
Finish: build setup for percolator-3.05-10.fc38.src.rpm
Start: rpmbuild percolator-3.05-10.fc38.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1658448000
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.2DdFkb
+ 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.RQ5F4u
+ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
~/build/BUILD/percolator-rel-3-05/percolator ~/build/BUILD/percolator-rel-3-05
+ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ mkdir -p percolator
+ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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=x86_64 ..
-- 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 = x86_64
-- 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/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=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/usr/bin/make  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build
/usr/bin/make  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build
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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/MyException.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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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/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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/picked_protein/ProteinPeptideIterator.cpp
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/usr/bin/ar qc libpicked_protein.a CMakeFiles/picked_protein.dir/__/Globals.cpp.o CMakeFiles/picked_protein.dir/__/Logger.cpp.o CMakeFiles/picked_protein.dir/__/MyException.cpp.o CMakeFiles/picked_protein.dir/__/Option.cpp.o CMakeFiles/picked_protein.dir/Database.cpp.o CMakeFiles/picked_protein.dir/Peptide.cpp.o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o CMakeFiles/picked_protein.dir/Protein.cpp.o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
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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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
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/usr/bin/ranlib libblas.a
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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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[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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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[ 30%] Building CXX object src/CMakeFiles/perclibrary.dir/parser.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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
/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);
      |         ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 32%] Building CXX object src/CMakeFiles/perclibrary.dir/serializer.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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
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]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
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]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
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]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 46%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 48%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 49%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
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(doubmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
le, 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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/ProteinProbEstimator.h:34,
                 from /builddir/build/BUILD/percolator-rel-3-05/src/ProteinProbEstimator.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) :
      |   ^~~~~~~~~~~
/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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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) :
      |   ^~~~~~~~~~~
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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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/ProteinProbEstimator.h:34,
                 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/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'
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[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
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[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
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/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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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
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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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
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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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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) :
      |   ^~~~~~~~~~~
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[ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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++ 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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[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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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=x86_64 ../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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 25%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
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]: 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/fido'
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]: 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
+ popd
~/build/BUILD/percolator-rel-3-05
+ mkdir -p converters
+ pushd converters
~/build/BUILD/percolator-rel-3-05/converters ~/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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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=x86_64 ../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 = x86_64
-- 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=
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 && /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
/usr/bin/make  -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.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'
[  5%] Built target generate_perc_xsdfiles
make[1]: 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/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'
[  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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
/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_make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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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/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/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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
/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++ ) {
      |                                     ~~^~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 41%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -MF CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/converters/MSToolkit/MSConvertFile.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'
[ 43%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
/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++){
      |             ~^~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 45%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 47%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 49%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
/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]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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[ 50%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
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[ 40%] Building CXX object CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -MF CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o.d -o CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -c /builddir/build/BUILD/percolator-rel-3-05/converters/tandem2011.12.01.1.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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[ 52%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 56%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
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[ 54%] Building CXX object CMakeFiles/converters.dir/Reader.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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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;
      |                      ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 60%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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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[ 58%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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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[ 61%] Building CXX object CMakeFiles/converters.dir/MzidentmlReader.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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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) {
      |                           ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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[ 63%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 65%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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);
      |              ^~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 67%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 70%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
[ 72%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 74%] Linking CXX static library libMSToolkit.a
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/cmake -P CMakeFiles/MSToolkit.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-05/converters/MSToolkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/MSToolkit.dir/link.txt --verbose=1
/usr/bin/ar qc libMSToolkit.a CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o CMakeFiles/MSToolkit.dir/MSObject.cpp.o CMakeFiles/MSToolkit.dir/MSReader.cpp.o CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o CMakeFiles/MSToolkit.dir/crawutils.cpp.o CMakeFiles/MSToolkit.dir/msmat.cpp.o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o
/usr/bin/ranlib libMSToolkit.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 74%] Built target MSToolkit
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 69%] 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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;
      |            ^~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
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[ 78%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabase.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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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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/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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In function 'strchr',
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/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);
      |                           ^
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lto1: note: source object is likely at address zero
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    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
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/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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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=x86_64 ../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 = x86_64
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Found Boost: /usr/lib64/cmake/Boost-1.78.0/BoostConfig.cmake (found version "1.78.0")  
-- 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
    CMAKE_USE_RELATIVE_PATHS
    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/elude
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
/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
/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'
[  8%] Building CXX object CMakeFiles/eludelibrary.dir/RetentionFeatures.cpp.o
/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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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'
/builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/RetentionFeatures.cpp: In static member function 'static double RetentionFeatures::IndexN(const std::string&, const std::map<std::__cxx11::basic_string<char>, double>&)':
/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();
      |                     ^~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 13%] Building CXX object CMakeFiles/eludelibrary.dir/EludeMain.cpp.o
/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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/EludeMain.cpp.o -MF CMakeFiles/eludelibrary.dir/EludeMain.cpp.o.d -o CMakeFiles/eludelibrary.dir/EludeMain.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/EludeMain.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 17%] Building CXX object CMakeFiles/eludelibrary.dir/LibSVRModel.cpp.o
/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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
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;
      |   ~~~~~make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
~~~~~~~~~~~~~^~~~~~~~
/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'
[ 21%] Building CXX object CMakeFiles/eludelibrary.dir/LibsvmWrapper.cpp.o
/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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
/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;
      |       ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[  8%] Building CXX object CMakeFiles/eludelibrary.dir/DataManager.cpp.o
/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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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();
      |       ^~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 26%] Building CXX object CMakeFiles/eludelibrary.dir/RetentionModel.cpp.o
/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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
/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;
      |                        ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/elude'
[ 34%] Building CXX object CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o
/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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o -MF CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o.d -o CMakeFiles/eludelibrary.dir/LTSRegression.cpp.o -c /builddir/build/BUILD/percolator-rel-3-05/src/elude_tool/LTSRegression.cpp
/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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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
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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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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/usr/bin/ranlib libeludelibrary.a
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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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I../src -I/usr/include/tirpc -O3 -DNDEBUG -MD -MT CMakeFiles/elude.dir/EludeCaller.cpp.o -MF CMakeFiles/elude.dir/EludeCaller.cpp.o.d -o CMakeFiles/elude.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) {
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 
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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.RVCWmB
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64
++ dirname /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64
+ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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.x86_64 'INSTALL=/usr/bin/install -p' -C percolator
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/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
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/usr/bin/make  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.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=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/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'
make[2]: Nothing to be done for 'src/CMakeFiles/perclibrary.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 60%] Built target perclibrary
/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/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=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/usr/bin/make  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Nothing to be done for 'src/picked_protein/CMakeFiles/picked_protein.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 76%] Built target picked_protein
/usr/bin/make  -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.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/blas /builddir/build/BUILD/percolator-rel-3-05/percolator /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas /builddir/build/BUILD/percolator-rel-3-05/percolator/src/blas/CMakeFiles/blas.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/usr/bin/make  -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Nothing to be done for 'src/blas/CMakeFiles/blas.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 84%] Built target blas
/usr/bin/make  -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.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/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'
/usr/bin/make  -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Nothing to be done for 'src/fido/CMakeFiles/fido.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 94%] Built target fido
/usr/bin/make  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.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/percolator.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/usr/bin/make  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Nothing to be done for 'src/CMakeFiles/percolator.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
[ 97%] Built target percolator
/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=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
/usr/bin/make  -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
make[2]: Nothing to be done for 'src/qvality/CMakeFiles/qvality.dir/build'.
make[2]: Leaving 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'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-05/percolator/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/percolator'
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.x86_64/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/percolator
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/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.x86_64 'INSTALL=/usr/bin/install -p' -C converters
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/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
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.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/perclibrary_part.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/perclibrary_part.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 23%] Built target perclibrary_part
/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=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 27%] Built target generate_perc_xsdfiles
/usr/bin/make  -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.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/converters.dir/DependInfo.cmake --color=
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
/usr/bin/make  -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
make[2]: Nothing to be done for 'CMakeFiles/converters.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-05/converters'
[ 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.x86_64/usr/bin/msgf2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/sqt2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/tandem2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/percolator/xml-1-1/mzIdentML1.1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/percolator/xml-2011.12.01.1/gaml_tandem1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/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.x86_64 '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.x86_64/usr/bin/elude
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/yeast_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/yeast_40.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/yeast_20.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/tfa.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_240.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_180.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Luna_120.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_90.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_60.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_240.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/elude/models/Jupiter_180.model
-- Installing: /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/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.x86_64/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.x86_64/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.x86_64/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.x86_64/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.x86_64/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.x86_64/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.x86_64/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.x86_64/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.x86_64/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.x86_64/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.x86_64/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.x86_64 --unique-debug-src-base percolator-3.05-10.fc38.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/percolator-rel-3-05
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/msgf2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/elude
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/percolator
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/qvality
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/sqt2pin
extracting debug info from /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/bin/tandem2pin
original debug info size: 83456kB, size after compression: 67668kB
/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.x86_64/src/serializer.hxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/src/serializer.cxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/src/parser.hxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/src/parser.cxx is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/percolator/src/Globals.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/elude/Globals.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/percolator-3.05-10.fc38.x86_64/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.M8JPOI
+ 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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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  -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-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 65f335fb382d42a187c03d2c60a5598e
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 Tue Dec 27 05:31:34 2022
 on 65f335fb382d42a187c03d2c60a5598e
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 0.410924 cpu seconds or 0 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 26.73 cpu seconds or 15 seconds wall clock time.
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: percolator-3.05-10.fc38.x86_64
Provides: percolator = 3.05-10.fc38 percolator(x86-64) = 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_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(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_2.2.5)(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.H6sePX
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/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.x86_64/usr/share/doc/percolator-data
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/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.x86_64/usr/share/doc/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.oSomQj
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/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.x86_64/usr/share/licenses/percolator-data
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-data
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/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.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.ACUniJ
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/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.x86_64/usr/share/doc/percolator-static
+ cp -pr ReadMe.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/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.x86_64/usr/share/doc/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.SBhmwQ
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/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.x86_64/usr/share/licenses/percolator-static
+ cp -pr license.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-static
+ cp -pr RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64/usr/share/licenses/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-static = 3.05-10.fc38 percolator-static(x86-64) = 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.x86_64
Provides: percolator-debugsource = 3.05-10.fc38 percolator-debugsource(x86-64) = 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.x86_64
Provides: debuginfo(build-id) = 14e1b941adb333f8f5bf9b9b775b47b7cda0ddb8 debuginfo(build-id) = 25dec41cf530400321dd3057cf1ca46069b8dfc9 debuginfo(build-id) = 3f25b1baaaec7545f433b743e8c6bdaf512abe97 debuginfo(build-id) = 53ad868eea8beb788eb88ad64b30fb879350599f debuginfo(build-id) = c43d08589bba9cd3f4c8feef3788468d12d16cdd debuginfo(build-id) = d79508577b118708a375ee1929c7a2e061fe27ac percolator-debuginfo = 3.05-10.fc38 percolator-debuginfo(x86-64) = 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(x86-64) = 3.05-10.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64
Wrote: /builddir/build/RPMS/percolator-static-3.05-10.fc38.x86_64.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.05-10.fc38.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-3.05-10.fc38.x86_64.rpm
Wrote: /builddir/build/RPMS/percolator-debugsource-3.05-10.fc38.x86_64.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.05-10.fc38.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.6cCahI
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-05
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/percolator-3.05-10.fc38.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.u23wIz
+ 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-x86_64-1672118612.989016/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-x86_64-1672118612.989016/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-x86_64-1672118612.989016/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/percolator-3.05-10.fc38.src.rpm) Config(child) 7 minutes 45 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