Warning: Permanently added '150.239.212.120' (ED25519) to the list of known hosts.

You can reproduce this build on your computer by running:

  sudo dnf install copr-rpmbuild
  /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/6745794-fedora-rawhide-s390x --chroot fedora-rawhide-s390x


Version: 0.70
PID: 6204
Logging PID: 6205
Task:
{'appstream': False,
 'background': True,
 'build_id': 6745794,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-s390x',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '11226bca0e38582fb7a7b15ee4795bb45f34f52c',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ppalka/boost-1.83-all-arches/percolator',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'percolator',
 'package_version': '3.06.04-1',
 'project_dirname': 'boost-1.83-all-arches',
 'project_name': 'boost-1.83-all-arches',
 'project_owner': 'ppalka',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ppalka/boost-1.83-all-arches/fedora-rawhide-s390x/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'ppalka/boost-1.83-all-arches--ppalka',
 'source_json': {},
 'source_type': None,
 'submitter': 'ppalka',
 'tags': [],
 'task_id': '6745794-fedora-rawhide-s390x',
 'timeout': 115200,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ppalka/boost-1.83-all-arches/percolator /var/lib/copr-rpmbuild/workspace/workdir-bg5dzm32/percolator --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ppalka/boost-1.83-all-arches/percolator', '/var/lib/copr-rpmbuild/workspace/workdir-bg5dzm32/percolator', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-bg5dzm32/percolator'...

Running: git checkout 11226bca0e38582fb7a7b15ee4795bb45f34f52c --

cmd: ['git', 'checkout', '11226bca0e38582fb7a7b15ee4795bb45f34f52c', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-bg5dzm32/percolator
rc: 0
stdout: 
stderr: Note: switching to '11226bca0e38582fb7a7b15ee4795bb45f34f52c'.

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 11226bc automatic import of percolator

Running: copr-distgit-client sources
/usr/bin/tail: 
cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-bg5dzm32/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-3-06-04.tar.gz
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o percolator-rel-3-06-04.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/ppalka/boost-1.83-all-arches/percolator/percolator-rel-3-06-04.tar.gz/md5/e49b456754b0ee11706ca799cf511582/percolator-rel-3-06-04.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 5157k  100 5157k    0     0  30.1M      0 --:--:-- --:--:-- --:--:-- 30.3M
INFO: Reading stdout from command: md5sum percolator-rel-3-06-04.tar.gz
INFO: Downloading yeast-01.sqt.tar.gz
INFO: Calling: curl -H Pragma: -o yeast-01.sqt.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/ppalka/boost-1.83-all-arches/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
/var/lib/copr-rpmbuild/main.log: file truncated
100 47.9M  100 47.9M    0     0  39.3M      0  0:00:01  0:00:01 --:--:-- 39.3M
INFO: Reading stdout from command: md5sum yeast-01.sqt.tar.gz

Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-bg5dzm32/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-bg5dzm32/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1702546936.417971 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.2 starting (python version = 3.11.3, NVR = mock-5.2-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-bg5dzm32/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-bg5dzm32/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1702546936.417971 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-bg5dzm32/percolator/percolator.spec)  Config(fedora-rawhide-s390x)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.2
INFO: Mock Version: 5.2
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1702546936.417971/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide
INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide
INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-s390x-bootstrap-1702546936.417971/root
INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture
INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount
INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/1dcc8587651e7b062fe2a5b463ae8981bff61ec4f02b37098f8dca28c3fac419/merged
INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/1dcc8587651e7b062fe2a5b463ae8981bff61ec4f02b37098f8dca28c3fac419/merged) with podman image umount
INFO: Package manager dnf detected and used (fallback)
INFO: Bootstrap image not marked ready
Start(bootstrap): installing dnf tooling
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                 2.7 MB/s | 4.0 MB     00:01    
fedora                                           10 MB/s |  63 MB     00:06    
Last metadata expiration check: 0:00:01 ago on Thu Dec 14 09:42:44 2023.
Package python3-dnf-4.18.2-1.fc40.noarch is already installed.
Dependencies resolved.
================================================================================
 Package                      Arch       Version               Repository  Size
================================================================================
Installing:
 python3-dnf-plugins-core     noarch     4.4.4-1.fc40          fedora     317 k
Installing dependencies:
 dbus-libs                    s390x      1:1.14.10-1.fc40      fedora     159 k
 python3-dateutil             noarch     1:2.8.2-11.fc40       fedora     356 k
 python3-dbus                 s390x      1.3.2-4.fc39          fedora     157 k
 python3-distro               noarch     1.8.0-6.fc39          fedora      49 k
 python3-six                  noarch     1.16.0-12.fc39        fedora      41 k
 python3-systemd              s390x      235-5.fc39            fedora     106 k

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

Total download size: 1.2 M
Installed size: 3.6 M
Downloading Packages:
(1/7): python3-dbus-1.3.2-4.fc39.s390x.rpm      1.7 MB/s | 157 kB     00:00    
(2/7): dbus-libs-1.14.10-1.fc40.s390x.rpm       1.5 MB/s | 159 kB     00:00    
(3/7): python3-dateutil-2.8.2-11.fc40.noarch.rp 3.2 MB/s | 356 kB     00:00    
(4/7): python3-distro-1.8.0-6.fc39.noarch.rpm   2.6 MB/s |  49 kB     00:00    
(5/7): python3-systemd-235-5.fc39.s390x.rpm     3.4 MB/s | 106 kB     00:00    
(6/7): python3-six-1.16.0-12.fc39.noarch.rpm    1.2 MB/s |  41 kB     00:00    
(7/7): python3-dnf-plugins-core-4.4.4-1.fc40.no 6.0 MB/s | 317 kB     00:00    
--------------------------------------------------------------------------------
Total                                           4.5 MB/s | 1.2 MB     00:00     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
  Installing       : python3-systemd-235-5.fc39.s390x                       1/7 
  Installing       : python3-six-1.16.0-12.fc39.noarch                      2/7 
  Installing       : python3-dateutil-1:2.8.2-11.fc40.noarch                3/7 
  Installing       : python3-distro-1.8.0-6.fc39.noarch                     4/7 
  Installing       : dbus-libs-1:1.14.10-1.fc40.s390x                       5/7 
  Installing       : python3-dbus-1.3.2-4.fc39.s390x                        6/7 
  Installing       : python3-dnf-plugins-core-4.4.4-1.fc40.noarch           7/7 
  Running scriptlet: python3-dnf-plugins-core-4.4.4-1.fc40.noarch           7/7 

Installed:
  dbus-libs-1:1.14.10-1.fc40.s390x                                              
  python3-dateutil-1:2.8.2-11.fc40.noarch                                       
  python3-dbus-1.3.2-4.fc39.s390x                                               
  python3-distro-1.8.0-6.fc39.noarch                                            
  python3-dnf-plugins-core-4.4.4-1.fc40.noarch                                  
  python3-six-1.16.0-12.fc39.noarch                                             
  python3-systemd-235-5.fc39.s390x                                              

Complete!
Finish(bootstrap): installing dnf tooling
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1702546936.417971/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf detected and used (direct choice)
Start: installing minimal buildroot with dnf
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                 632 kB/s | 4.0 MB     00:06    
fedora                                          9.7 MB/s |  63 MB     00:06    
Last metadata expiration check: 0:00:01 ago on Thu Dec 14 09:43:30 2023.
Dependencies resolved.
================================================================================
 Package                      Arch   Version                    Repo       Size
================================================================================
Installing group/module packages:
 bash                         s390x  5.2.21-2.fc40              fedora    1.8 M
 bzip2                        s390x  1.0.8-16.fc39              fedora     53 k
 coreutils                    s390x  9.4-1.fc40                 fedora    1.2 M
 cpio                         s390x  2.14-5.fc40                fedora    283 k
 diffutils                    s390x  3.10-3.fc39                fedora    407 k
 fedora-release-common        noarch 40-0.20                    fedora     20 k
 findutils                    s390x  1:4.9.0-6.fc40             fedora    497 k
 gawk                         s390x  5.2.2-2.fc39               fedora    1.1 M
 glibc-minimal-langpack       s390x  2.38.9000-27.fc40          fedora     86 k
 grep                         s390x  3.11-5.fc40                fedora    305 k
 gzip                         s390x  1.12-6.fc39                fedora    173 k
 info                         s390x  7.1-1.fc40                 fedora    195 k
 patch                        s390x  2.7.6-22.fc39              fedora    134 k
 redhat-rpm-config            noarch 271-1.fc40                 fedora     81 k
 rpm-build                    s390x  4.19.1-1.fc40              fedora     79 k
 sed                          s390x  4.8-14.fc39                fedora    309 k
 shadow-utils                 s390x  2:4.14.0-2.fc40            fedora    1.3 M
 tar                          s390x  2:1.35-2.fc40              fedora    874 k
 unzip                        s390x  6.0-62.fc39                fedora    194 k
 util-linux                   s390x  2.39.2-1.fc40              fedora    1.1 M
 which                        s390x  2.21-40.fc39               fedora     43 k
 xz                           s390x  5.4.5-1.fc40               fedora    558 k
Installing dependencies:
 alternatives                 s390x  1.25-1.fc39                fedora     39 k
 ansible-srpm-macros          noarch 1-11.fc39                  fedora     21 k
 audit-libs                   s390x  3.1.2-5.fc40               fedora    121 k
 authselect                   s390x  1.4.3-1.fc40               fedora    149 k
 authselect-libs              s390x  1.4.3-1.fc40               fedora    248 k
 basesystem                   noarch 11-18.fc39                 fedora    7.2 k
 binutils                     s390x  2.41-16.fc40               fedora    5.9 M
 binutils-gold                s390x  2.41-16.fc40               fedora    991 k
 bzip2-libs                   s390x  1.0.8-16.fc39              fedora     46 k
 ca-certificates              noarch 2023.2.62_v7.0.401-4.fc40  fedora    863 k
 coreutils-common             s390x  9.4-1.fc40                 fedora    2.1 M
 cracklib                     s390x  2.9.11-2.fc39              fedora     94 k
 crypto-policies              noarch 20231204-1.git1e3a2e4.fc40 fedora    100 k
 curl                         s390x  8.5.0-1.fc40               fedora    372 k
 cyrus-sasl-lib               s390x  2.1.28-11.fc39             fedora    819 k
 debugedit                    s390x  5.0-12.fc40                fedora     81 k
 dwz                          s390x  0.15-3.fc39                fedora    144 k
 ed                           s390x  1.19-4.fc39                fedora     80 k
 efi-srpm-macros              noarch 5-9.fc39                   fedora     22 k
 elfutils                     s390x  0.190-4.fc40               fedora    576 k
 elfutils-debuginfod-client   s390x  0.190-4.fc40               fedora     38 k
 elfutils-default-yama-scope  noarch 0.190-4.fc40               fedora     13 k
 elfutils-libelf              s390x  0.190-4.fc40               fedora    200 k
 elfutils-libs                s390x  0.190-4.fc40               fedora    276 k
 fedora-gpg-keys              noarch 40-0.2                     fedora    130 k
 fedora-release               noarch 40-0.20                    fedora    9.3 k
 fedora-release-identity-basic
                              noarch 40-0.20                    fedora     10 k
 fedora-repos                 noarch 40-0.2                     fedora    9.3 k
 fedora-repos-rawhide         noarch 40-0.2                     fedora    8.9 k
 file                         s390x  5.45-1.fc40                fedora     49 k
 file-libs                    s390x  5.45-1.fc40                fedora    769 k
 filesystem                   s390x  3.18-6.fc39                fedora    1.1 M
 fonts-srpm-macros            noarch 1:2.0.5-12.fc39            fedora     26 k
 forge-srpm-macros            noarch 0.2.0-1.fc40               fedora     18 k
 fpc-srpm-macros              noarch 1.3-8.fc39                 fedora    7.4 k
 gdb-minimal                  s390x  14.1-1.fc40                copr_base 4.1 M
 gdbm                         s390x  1:1.23-4.fc39              fedora    156 k
 gdbm-libs                    s390x  1:1.23-4.fc39              fedora     58 k
 ghc-srpm-macros              noarch 1.6.1-3.fc40               fedora    8.1 k
 glibc                        s390x  2.38.9000-27.fc40          fedora    1.9 M
 glibc-common                 s390x  2.38.9000-27.fc40          fedora    386 k
 glibc-gconv-extra            s390x  2.38.9000-27.fc40          fedora    1.7 M
 gmp                          s390x  1:6.2.1-5.fc39             fedora    325 k
 gnat-srpm-macros             noarch 6-3.fc39                   fedora    8.8 k
 go-srpm-macros               noarch 3.3.1-1.fc40               fedora     28 k
 jansson                      s390x  2.13.1-7.fc39              fedora     44 k
 kernel-srpm-macros           noarch 1.0-20.fc39                fedora     10 k
 keyutils-libs                s390x  1.6.1-7.fc39               fedora     31 k
 krb5-libs                    s390x  1.21.2-2.fc40              fedora    780 k
 libacl                       s390x  2.3.1-11.fc40              fedora     25 k
 libarchive                   s390x  3.7.2-1.fc40               fedora    440 k
 libattr                      s390x  2.5.1-9.fc40               fedora     18 k
 libblkid                     s390x  2.39.2-1.fc40              fedora    120 k
 libbrotli                    s390x  1.1.0-1.fc40               fedora    379 k
 libcap                       s390x  2.69-1.fc40                fedora     85 k
 libcap-ng                    s390x  0.8.3-8.fc40               fedora     32 k
 libcom_err                   s390x  1.47.0-2.fc39              fedora     26 k
 libcurl                      s390x  8.5.0-1.fc40               fedora    362 k
 libeconf                     s390x  0.5.2-1.fc40               fedora     32 k
 libevent                     s390x  2.1.12-9.fc39              fedora    260 k
 libfdisk                     s390x  2.39.2-1.fc40              fedora    165 k
 libffi                       s390x  3.4.4-4.fc39               fedora     36 k
 libgcc                       s390x  13.2.1-6.fc40              fedora     85 k
 libgomp                      s390x  13.2.1-6.fc40              fedora    325 k
 libidn2                      s390x  2.3.4-3.fc39               fedora    118 k
 libmount                     s390x  2.39.2-1.fc40              fedora    158 k
 libnghttp2                   s390x  1.58.0-1.fc40              fedora     78 k
 libnsl2                      s390x  2.0.0-6.fc39               fedora     30 k
 libpkgconf                   s390x  1.9.5-2.fc39               fedora     38 k
 libpsl                       s390x  0.21.2-4.fc39              fedora     63 k
 libpwquality                 s390x  1.4.5-6.fc39               fedora    121 k
 libselinux                   s390x  3.6-0.rc2.1.fc40           fedora     92 k
 libsemanage                  s390x  3.6-0.rc2.1.fc40           fedora    119 k
 libsepol                     s390x  3.6-0.rc2.1.fc40           fedora    346 k
 libsigsegv                   s390x  2.14-5.fc39                fedora     27 k
 libsmartcols                 s390x  2.39.2-1.fc40              fedora     70 k
 libssh                       s390x  0.10.5-2.fc39              fedora    209 k
 libssh-config                noarch 0.10.5-2.fc39              fedora    9.2 k
 libstdc++                    s390x  13.2.1-6.fc40              fedora    953 k
 libtasn1                     s390x  4.19.0-3.fc39              fedora     77 k
 libtirpc                     s390x  1.3.4-0.fc40               fedora     96 k
 libunistring                 s390x  1.1-5.fc40                 fedora    556 k
 libutempter                  s390x  1.2.1-10.fc39              fedora     26 k
 libuuid                      s390x  2.39.2-1.fc40              fedora     28 k
 libverto                     s390x  0.3.2-6.fc39               fedora     21 k
 libxcrypt                    s390x  4.4.36-2.fc39              fedora    124 k
 libxml2                      s390x  2.12.3-1.fc40              fedora    705 k
 libzstd                      s390x  1.5.5-4.fc39               fedora    342 k
 lua-libs                     s390x  5.4.6-3.fc39               fedora    142 k
 lua-srpm-macros              noarch 1-9.fc39                   fedora    8.6 k
 lz4-libs                     s390x  1.9.4-4.fc39               fedora     81 k
 mpfr                         s390x  4.2.1-1.fc40               fedora    297 k
 ncurses-base                 noarch 6.4-8.20231001.fc40        fedora     88 k
 ncurses-libs                 s390x  6.4-8.20231001.fc40        fedora    362 k
 ocaml-srpm-macros            noarch 9-1.fc40                   fedora    9.0 k
 openblas-srpm-macros         noarch 2-14.fc39                  fedora    7.5 k
 openldap                     s390x  2.6.6-1.fc39               fedora    262 k
 openssl-libs                 s390x  1:3.1.4-1.fc40             fedora    1.9 M
 p11-kit                      s390x  0.25.3-1.fc40              fedora    533 k
 p11-kit-trust                s390x  0.25.3-1.fc40              fedora    142 k
 package-notes-srpm-macros    noarch 0.5-9.fc39                 fedora     11 k
 pam                          s390x  1.5.3-8.fc40               fedora    557 k
 pam-libs                     s390x  1.5.3-8.fc40               fedora     59 k
 pcre2                        s390x  10.42-2.fc40               fedora    250 k
 pcre2-syntax                 noarch 10.42-2.fc40               fedora    143 k
 perl-srpm-macros             noarch 1-51.fc39                  fedora    8.0 k
 pkgconf                      s390x  1.9.5-2.fc39               fedora     43 k
 pkgconf-m4                   noarch 1.9.5-2.fc39               fedora     14 k
 pkgconf-pkg-config           s390x  1.9.5-2.fc39               fedora    9.6 k
 popt                         s390x  1.19-3.fc39                fedora     69 k
 publicsuffix-list-dafsa      noarch 20230812-1.fc40            fedora     57 k
 pyproject-srpm-macros        noarch 1.10.0-1.fc40              fedora     14 k
 python-srpm-macros           noarch 3.12-5.fc40                fedora     25 k
 qt5-srpm-macros              noarch 5.15.11-1.fc40             fedora    8.3 k
 qt6-srpm-macros              noarch 6.6.1-1.fc40               fedora    8.6 k
 readline                     s390x  8.2-4.fc39                 fedora    229 k
 rpm                          s390x  4.19.1-1.fc40              fedora    537 k
 rpm-build-libs               s390x  4.19.1-1.fc40              fedora     97 k
 rpm-libs                     s390x  4.19.1-1.fc40              fedora    324 k
 rpm-sequoia                  s390x  1.5.0-2.fc40               fedora    1.0 M
 rust-srpm-macros             noarch 25.2-2.fc40                fedora     13 k
 setup                        noarch 2.14.5-1.fc40              fedora    155 k
 sqlite-libs                  s390x  3.44.2-1.fc40              fedora    742 k
 systemd-libs                 s390x  255-1.fc40                 fedora    711 k
 util-linux-core              s390x  2.39.2-1.fc40              fedora    496 k
 xxhash-libs                  s390x  0.8.2-1.fc39               fedora     37 k
 xz-libs                      s390x  5.4.5-1.fc40               fedora    114 k
 zip                          s390x  3.0-39.fc40                fedora    283 k
 zlib                         s390x  1.2.13-5.fc40              fedora    101 k
 zstd                         s390x  1.5.5-4.fc39               fedora    506 k
Installing Groups:
 Buildsystem building group                                                    

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

Total download size: 52 M
Installed size: 178 M
Downloading Packages:
(1/152): ansible-srpm-macros-1-11.fc39.noarch.r 111 kB/s |  21 kB     00:00    
(2/152): alternatives-1.25-1.fc39.s390x.rpm     181 kB/s |  39 kB     00:00    
(3/152): gdb-minimal-14.1-1.fc40.s390x.rpm       12 MB/s | 4.1 MB     00:00    
(4/152): audit-libs-3.1.2-5.fc40.s390x.rpm      599 kB/s | 121 kB     00:00    
(5/152): authselect-1.4.3-1.fc40.s390x.rpm      719 kB/s | 149 kB     00:00    
(6/152): basesystem-11-18.fc39.noarch.rpm       116 kB/s | 7.2 kB     00:00    
(7/152): bash-5.2.21-2.fc40.s390x.rpm           6.2 MB/s | 1.8 MB     00:00    
(8/152): authselect-libs-1.4.3-1.fc40.s390x.rpm 603 kB/s | 248 kB     00:00    
(9/152): binutils-gold-2.41-16.fc40.s390x.rpm    12 MB/s | 991 kB     00:00    
(10/152): bzip2-1.0.8-16.fc39.s390x.rpm         733 kB/s |  53 kB     00:00    
(11/152): binutils-2.41-16.fc40.s390x.rpm        14 MB/s | 5.9 MB     00:00    
(12/152): bzip2-libs-1.0.8-16.fc39.s390x.rpm    704 kB/s |  46 kB     00:00    
(13/152): coreutils-9.4-1.fc40.s390x.rpm         16 MB/s | 1.2 MB     00:00    
(14/152): coreutils-common-9.4-1.fc40.s390x.rpm  19 MB/s | 2.1 MB     00:00    
(15/152): cpio-2.14-5.fc40.s390x.rpm            4.4 MB/s | 283 kB     00:00    
(16/152): ca-certificates-2023.2.62_v7.0.401-4. 4.1 MB/s | 863 kB     00:00    
(17/152): cracklib-2.9.11-2.fc39.s390x.rpm      1.5 MB/s |  94 kB     00:00    
(18/152): crypto-policies-20231204-1.git1e3a2e4 1.6 MB/s | 100 kB     00:00    
(19/152): curl-8.5.0-1.fc40.s390x.rpm           4.5 MB/s | 372 kB     00:00    
(20/152): cyrus-sasl-lib-2.1.28-11.fc39.s390x.r  11 MB/s | 819 kB     00:00    
(21/152): debugedit-5.0-12.fc40.s390x.rpm       1.3 MB/s |  81 kB     00:00    
(22/152): dwz-0.15-3.fc39.s390x.rpm             2.2 MB/s | 144 kB     00:00    
(23/152): ed-1.19-4.fc39.s390x.rpm              1.3 MB/s |  80 kB     00:00    
(24/152): diffutils-3.10-3.fc39.s390x.rpm       4.9 MB/s | 407 kB     00:00    
(25/152): efi-srpm-macros-5-9.fc39.noarch.rpm   366 kB/s |  22 kB     00:00    
(26/152): elfutils-0.190-4.fc40.s390x.rpm       8.4 MB/s | 576 kB     00:00    
(27/152): elfutils-debuginfod-client-0.190-4.fc 588 kB/s |  38 kB     00:00    
(28/152): elfutils-default-yama-scope-0.190-4.f 212 kB/s |  13 kB     00:00    
(29/152): elfutils-libelf-0.190-4.fc40.s390x.rp 3.1 MB/s | 200 kB     00:00    
(30/152): elfutils-libs-0.190-4.fc40.s390x.rpm  3.6 MB/s | 276 kB     00:00    
(31/152): fedora-gpg-keys-40-0.2.noarch.rpm     2.0 MB/s | 130 kB     00:00    
(32/152): fedora-release-40-0.20.noarch.rpm     149 kB/s | 9.3 kB     00:00    
(33/152): fedora-release-common-40-0.20.noarch. 312 kB/s |  20 kB     00:00    
(34/152): fedora-release-identity-basic-40-0.20 165 kB/s |  10 kB     00:00    
(35/152): fedora-repos-40-0.2.noarch.rpm        156 kB/s | 9.3 kB     00:00    
(36/152): fedora-repos-rawhide-40-0.2.noarch.rp 137 kB/s | 8.9 kB     00:00    
(37/152): file-5.45-1.fc40.s390x.rpm            659 kB/s |  49 kB     00:00    
(38/152): file-libs-5.45-1.fc40.s390x.rpm        11 MB/s | 769 kB     00:00    
(39/152): fonts-srpm-macros-2.0.5-12.fc39.noarc 418 kB/s |  26 kB     00:00    
(40/152): filesystem-3.18-6.fc39.s390x.rpm      9.3 MB/s | 1.1 MB     00:00    
(41/152): findutils-4.9.0-6.fc40.s390x.rpm      6.9 MB/s | 497 kB     00:00    
(42/152): fpc-srpm-macros-1.3-8.fc39.noarch.rpm 121 kB/s | 7.4 kB     00:00    
(43/152): forge-srpm-macros-0.2.0-1.fc40.noarch 201 kB/s |  18 kB     00:00    
(44/152): gawk-5.2.2-2.fc39.s390x.rpm            11 MB/s | 1.1 MB     00:00    
(45/152): gdbm-1.23-4.fc39.s390x.rpm            2.4 MB/s | 156 kB     00:00    
(46/152): gdbm-libs-1.23-4.fc39.s390x.rpm       925 kB/s |  58 kB     00:00    
(47/152): ghc-srpm-macros-1.6.1-3.fc40.noarch.r 128 kB/s | 8.1 kB     00:00    
(48/152): glibc-common-2.38.9000-27.fc40.s390x. 5.5 MB/s | 386 kB     00:00    
(49/152): glibc-2.38.9000-27.fc40.s390x.rpm      18 MB/s | 1.9 MB     00:00    
(50/152): glibc-minimal-langpack-2.38.9000-27.f 1.4 MB/s |  86 kB     00:00    
(51/152): glibc-gconv-extra-2.38.9000-27.fc40.s  14 MB/s | 1.7 MB     00:00    
(52/152): gmp-6.2.1-5.fc39.s390x.rpm            4.8 MB/s | 325 kB     00:00    
(53/152): gnat-srpm-macros-6-3.fc39.noarch.rpm  147 kB/s | 8.8 kB     00:00    
(54/152): go-srpm-macros-3.3.1-1.fc40.noarch.rp 414 kB/s |  28 kB     00:00    
(55/152): grep-3.11-5.fc40.s390x.rpm            4.3 MB/s | 305 kB     00:00    
(56/152): gzip-1.12-6.fc39.s390x.rpm            2.7 MB/s | 173 kB     00:00    
(57/152): jansson-2.13.1-7.fc39.s390x.rpm       724 kB/s |  44 kB     00:00    
(58/152): info-7.1-1.fc40.s390x.rpm             2.7 MB/s | 195 kB     00:00    
(59/152): kernel-srpm-macros-1.0-20.fc39.noarch 175 kB/s |  10 kB     00:00    
(60/152): keyutils-libs-1.6.1-7.fc39.s390x.rpm  511 kB/s |  31 kB     00:00    
(61/152): krb5-libs-1.21.2-2.fc40.s390x.rpm     9.3 MB/s | 780 kB     00:00    
(62/152): libacl-2.3.1-11.fc40.s390x.rpm        411 kB/s |  25 kB     00:00    
(63/152): libarchive-3.7.2-1.fc40.s390x.rpm     6.3 MB/s | 440 kB     00:00    
(64/152): libattr-2.5.1-9.fc40.s390x.rpm        287 kB/s |  18 kB     00:00    
(65/152): libblkid-2.39.2-1.fc40.s390x.rpm      1.9 MB/s | 120 kB     00:00    
(66/152): libbrotli-1.1.0-1.fc40.s390x.rpm      5.5 MB/s | 379 kB     00:00    
(67/152): libcap-2.69-1.fc40.s390x.rpm          1.3 MB/s |  85 kB     00:00    
(68/152): libcap-ng-0.8.3-8.fc40.s390x.rpm      539 kB/s |  32 kB     00:00    
(69/152): libcom_err-1.47.0-2.fc39.s390x.rpm    427 kB/s |  26 kB     00:00    
(70/152): libcurl-8.5.0-1.fc40.s390x.rpm        5.0 MB/s | 362 kB     00:00    
(71/152): libeconf-0.5.2-1.fc40.s390x.rpm       530 kB/s |  32 kB     00:00    
(72/152): libevent-2.1.12-9.fc39.s390x.rpm      3.7 MB/s | 260 kB     00:00    
(73/152): libffi-3.4.4-4.fc39.s390x.rpm         571 kB/s |  36 kB     00:00    
(74/152): libfdisk-2.39.2-1.fc40.s390x.rpm      2.4 MB/s | 165 kB     00:00    
(75/152): libgcc-13.2.1-6.fc40.s390x.rpm        1.3 MB/s |  85 kB     00:00    
(76/152): libgomp-13.2.1-6.fc40.s390x.rpm       4.9 MB/s | 325 kB     00:00    
(77/152): libidn2-2.3.4-3.fc39.s390x.rpm        1.8 MB/s | 118 kB     00:00    
(78/152): libmount-2.39.2-1.fc40.s390x.rpm      2.5 MB/s | 158 kB     00:00    
(79/152): libnghttp2-1.58.0-1.fc40.s390x.rpm    1.3 MB/s |  78 kB     00:00    
(80/152): libnsl2-2.0.0-6.fc39.s390x.rpm        468 kB/s |  30 kB     00:00    
(81/152): libpkgconf-1.9.5-2.fc39.s390x.rpm     625 kB/s |  38 kB     00:00    
(82/152): libpsl-0.21.2-4.fc39.s390x.rpm        1.0 MB/s |  63 kB     00:00    
(83/152): libpwquality-1.4.5-6.fc39.s390x.rpm   1.8 MB/s | 121 kB     00:00    
(84/152): libselinux-3.6-0.rc2.1.fc40.s390x.rpm 1.5 MB/s |  92 kB     00:00    
(85/152): libsemanage-3.6-0.rc2.1.fc40.s390x.rp 1.9 MB/s | 119 kB     00:00    
(86/152): libsepol-3.6-0.rc2.1.fc40.s390x.rpm   4.8 MB/s | 346 kB     00:00    
(87/152): libsigsegv-2.14-5.fc39.s390x.rpm      439 kB/s |  27 kB     00:00    
(88/152): libsmartcols-2.39.2-1.fc40.s390x.rpm  1.1 MB/s |  70 kB     00:00    
(89/152): libssh-0.10.5-2.fc39.s390x.rpm        2.9 MB/s | 209 kB     00:00    
(90/152): libssh-config-0.10.5-2.fc39.noarch.rp 145 kB/s | 9.2 kB     00:00    
(91/152): libstdc++-13.2.1-6.fc40.s390x.rpm      12 MB/s | 953 kB     00:00    
(92/152): libtasn1-4.19.0-3.fc39.s390x.rpm      1.2 MB/s |  77 kB     00:00    
(93/152): libtirpc-1.3.4-0.fc40.s390x.rpm       1.5 MB/s |  96 kB     00:00    
(94/152): libunistring-1.1-5.fc40.s390x.rpm     8.2 MB/s | 556 kB     00:00    
(95/152): libutempter-1.2.1-10.fc39.s390x.rpm   409 kB/s |  26 kB     00:00    
(96/152): libuuid-2.39.2-1.fc40.s390x.rpm       464 kB/s |  28 kB     00:00    
(97/152): libverto-0.3.2-6.fc39.s390x.rpm       345 kB/s |  21 kB     00:00    
(98/152): libxcrypt-4.4.36-2.fc39.s390x.rpm     1.8 MB/s | 124 kB     00:00    
(99/152): libxml2-2.12.3-1.fc40.s390x.rpm       9.4 MB/s | 705 kB     00:00    
(100/152): libzstd-1.5.5-4.fc39.s390x.rpm       5.1 MB/s | 342 kB     00:00    
(101/152): lua-libs-5.4.6-3.fc39.s390x.rpm      2.1 MB/s | 142 kB     00:00    
(102/152): lua-srpm-macros-1-9.fc39.noarch.rpm  142 kB/s | 8.6 kB     00:00    
(103/152): lz4-libs-1.9.4-4.fc39.s390x.rpm      934 kB/s |  81 kB     00:00    
(104/152): mpfr-4.2.1-1.fc40.s390x.rpm          3.6 MB/s | 297 kB     00:00    
(105/152): ncurses-base-6.4-8.20231001.fc40.noa 1.3 MB/s |  88 kB     00:00    
(106/152): openblas-srpm-macros-2-14.fc39.noarc 116 kB/s | 7.5 kB     00:00    
(107/152): ocaml-srpm-macros-9-1.fc40.noarch.rp 135 kB/s | 9.0 kB     00:00    
(108/152): ncurses-libs-6.4-8.20231001.fc40.s39 4.2 MB/s | 362 kB     00:00    
(109/152): openldap-2.6.6-1.fc39.s390x.rpm      3.9 MB/s | 262 kB     00:00    
(110/152): p11-kit-0.25.3-1.fc40.s390x.rpm      7.8 MB/s | 533 kB     00:00    
(111/152): openssl-libs-3.1.4-1.fc40.s390x.rpm   16 MB/s | 1.9 MB     00:00    
(112/152): p11-kit-trust-0.25.3-1.fc40.s390x.rp 2.2 MB/s | 142 kB     00:00    
(113/152): package-notes-srpm-macros-0.5-9.fc39 180 kB/s |  11 kB     00:00    
(114/152): pam-1.5.3-8.fc40.s390x.rpm           7.3 MB/s | 557 kB     00:00    
(115/152): pam-libs-1.5.3-8.fc40.s390x.rpm      960 kB/s |  59 kB     00:00    
(116/152): patch-2.7.6-22.fc39.s390x.rpm        2.1 MB/s | 134 kB     00:00    
(117/152): pcre2-10.42-2.fc40.s390x.rpm         3.7 MB/s | 250 kB     00:00    
(118/152): perl-srpm-macros-1-51.fc39.noarch.rp 134 kB/s | 8.0 kB     00:00    
(119/152): pcre2-syntax-10.42-2.fc40.noarch.rpm 2.1 MB/s | 143 kB     00:00    
(120/152): pkgconf-m4-1.9.5-2.fc39.noarch.rpm   231 kB/s |  14 kB     00:00    
(121/152): pkgconf-1.9.5-2.fc39.s390x.rpm       695 kB/s |  43 kB     00:00    
(122/152): pkgconf-pkg-config-1.9.5-2.fc39.s390 152 kB/s | 9.6 kB     00:00    
(123/152): publicsuffix-list-dafsa-20230812-1.f 948 kB/s |  57 kB     00:00    
(124/152): popt-1.19-3.fc39.s390x.rpm           1.1 MB/s |  69 kB     00:00    
(125/152): pyproject-srpm-macros-1.10.0-1.fc40. 226 kB/s |  14 kB     00:00    
(126/152): python-srpm-macros-3.12-5.fc40.noarc 413 kB/s |  25 kB     00:00    
(127/152): qt5-srpm-macros-5.15.11-1.fc40.noarc 138 kB/s | 8.3 kB     00:00    
(128/152): qt6-srpm-macros-6.6.1-1.fc40.noarch. 136 kB/s | 8.6 kB     00:00    
(129/152): readline-8.2-4.fc39.s390x.rpm        3.6 MB/s | 229 kB     00:00    
(130/152): redhat-rpm-config-271-1.fc40.noarch. 1.3 MB/s |  81 kB     00:00    
(131/152): rpm-4.19.1-1.fc40.s390x.rpm          7.1 MB/s | 537 kB     00:00    
(132/152): rpm-build-libs-4.19.1-1.fc40.s390x.r 1.6 MB/s |  97 kB     00:00    
(133/152): rpm-build-4.19.1-1.fc40.s390x.rpm    1.3 MB/s |  79 kB     00:00    
(134/152): rpm-libs-4.19.1-1.fc40.s390x.rpm     4.6 MB/s | 324 kB     00:00    
(135/152): rust-srpm-macros-25.2-2.fc40.noarch. 216 kB/s |  13 kB     00:00    
(136/152): rpm-sequoia-1.5.0-2.fc40.s390x.rpm    13 MB/s | 1.0 MB     00:00    
(137/152): sed-4.8-14.fc39.s390x.rpm            4.0 MB/s | 309 kB     00:00    
(138/152): setup-2.14.5-1.fc40.noarch.rpm       2.5 MB/s | 155 kB     00:00    
(139/152): shadow-utils-4.14.0-2.fc40.s390x.rpm  15 MB/s | 1.3 MB     00:00    
(140/152): sqlite-libs-3.44.2-1.fc40.s390x.rpm  9.2 MB/s | 742 kB     00:00    
(141/152): systemd-libs-255-1.fc40.s390x.rpm     10 MB/s | 711 kB     00:00    
(142/152): tar-1.35-2.fc40.s390x.rpm             11 MB/s | 874 kB     00:00    
(143/152): unzip-6.0-62.fc39.s390x.rpm          2.9 MB/s | 194 kB     00:00    
(144/152): util-linux-2.39.2-1.fc40.s390x.rpm    16 MB/s | 1.1 MB     00:00    
(145/152): util-linux-core-2.39.2-1.fc40.s390x. 7.0 MB/s | 496 kB     00:00    
(146/152): which-2.21-40.fc39.s390x.rpm         683 kB/s |  43 kB     00:00    
(147/152): xxhash-libs-0.8.2-1.fc39.s390x.rpm   611 kB/s |  37 kB     00:00    
(148/152): xz-libs-5.4.5-1.fc40.s390x.rpm       1.7 MB/s | 114 kB     00:00    
(149/152): xz-5.4.5-1.fc40.s390x.rpm            7.5 MB/s | 558 kB     00:00    
(150/152): zip-3.0-39.fc40.s390x.rpm            4.3 MB/s | 283 kB     00:00    
(151/152): zlib-1.2.13-5.fc40.s390x.rpm         1.5 MB/s | 101 kB     00:00    
(152/152): zstd-1.5.5-4.fc39.s390x.rpm          7.2 MB/s | 506 kB     00:00    
--------------------------------------------------------------------------------
Total                                           5.7 MB/s |  52 MB     00:09     
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0xA15B79CC:
 Userid     : "Fedora (40) <fedora-40-primary@fedoraproject.org>"
 Fingerprint: 115D F9AE F857 853E E844 5D0A 0727 707E A15B 79CC
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-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-40-primary (0xA15B79CC) is already installed
fedora                                          1.6 MB/s | 1.6 kB     00:00    
Importing GPG key 0x18B8E74C:
 Userid     : "Fedora (39) <fedora-39-primary@fedoraproject.org>"
 Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C
 From       : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.18-6.fc39.s390x                           1/1 
  Preparing        :                                                        1/1 
  Installing       : libgcc-13.2.1-6.fc40.s390x                           1/152 
  Running scriptlet: libgcc-13.2.1-6.fc40.s390x                           1/152 
  Installing       : crypto-policies-20231204-1.git1e3a2e4.fc40.noarc     2/152 
  Running scriptlet: crypto-policies-20231204-1.git1e3a2e4.fc40.noarc     2/152 
  Installing       : fedora-release-identity-basic-40-0.20.noarch         3/152 
  Installing       : fedora-repos-rawhide-40-0.2.noarch                   4/152 
  Installing       : fedora-gpg-keys-40-0.2.noarch                        5/152 
  Installing       : fedora-repos-40-0.2.noarch                           6/152 
  Installing       : fedora-release-common-40-0.20.noarch                 7/152 
  Installing       : fedora-release-40-0.20.noarch                        8/152 
  Installing       : setup-2.14.5-1.fc40.noarch                           9/152 
warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.14.5-1.fc40.noarch                           9/152 
  Installing       : filesystem-3.18-6.fc39.s390x                        10/152 
  Installing       : basesystem-11-18.fc39.noarch                        11/152 
  Installing       : rust-srpm-macros-25.2-2.fc40.noarch                 12/152 
  Installing       : qt6-srpm-macros-6.6.1-1.fc40.noarch                 13/152 
  Installing       : qt5-srpm-macros-5.15.11-1.fc40.noarch               14/152 
  Installing       : publicsuffix-list-dafsa-20230812-1.fc40.noarch      15/152 
  Installing       : pkgconf-m4-1.9.5-2.fc39.noarch                      16/152 
  Installing       : perl-srpm-macros-1-51.fc39.noarch                   17/152 
  Installing       : pcre2-syntax-10.42-2.fc40.noarch                    18/152 
  Installing       : package-notes-srpm-macros-0.5-9.fc39.noarch         19/152 
  Installing       : openblas-srpm-macros-2-14.fc39.noarch               20/152 
  Installing       : ocaml-srpm-macros-9-1.fc40.noarch                   21/152 
  Installing       : ncurses-base-6.4-8.20231001.fc40.noarch             22/152 
  Installing       : glibc-gconv-extra-2.38.9000-27.fc40.s390x           23/152 
  Running scriptlet: glibc-gconv-extra-2.38.9000-27.fc40.s390x           23/152 
  Installing       : glibc-minimal-langpack-2.38.9000-27.fc40.s390x      24/152 
  Installing       : glibc-common-2.38.9000-27.fc40.s390x                25/152 
  Running scriptlet: glibc-2.38.9000-27.fc40.s390x                       26/152 
  Installing       : glibc-2.38.9000-27.fc40.s390x                       26/152 
  Running scriptlet: glibc-2.38.9000-27.fc40.s390x                       26/152 
  Installing       : ncurses-libs-6.4-8.20231001.fc40.s390x              27/152 
  Installing       : bash-5.2.21-2.fc40.s390x                            28/152 
  Running scriptlet: bash-5.2.21-2.fc40.s390x                            28/152 
  Installing       : zlib-1.2.13-5.fc40.s390x                            29/152 
  Installing       : xz-libs-5.4.5-1.fc40.s390x                          30/152 
  Installing       : bzip2-libs-1.0.8-16.fc39.s390x                      31/152 
  Installing       : readline-8.2-4.fc39.s390x                           32/152 
  Installing       : libstdc++-13.2.1-6.fc40.s390x                       33/152 
  Installing       : libuuid-2.39.2-1.fc40.s390x                         34/152 
  Installing       : libzstd-1.5.5-4.fc39.s390x                          35/152 
  Installing       : elfutils-libelf-0.190-4.fc40.s390x                  36/152 
  Installing       : popt-1.19-3.fc39.s390x                              37/152 
  Installing       : libblkid-2.39.2-1.fc40.s390x                        38/152 
  Installing       : gmp-1:6.2.1-5.fc39.s390x                            39/152 
  Installing       : libattr-2.5.1-9.fc40.s390x                          40/152 
  Installing       : libacl-2.3.1-11.fc40.s390x                          41/152 
  Installing       : libxcrypt-4.4.36-2.fc39.s390x                       42/152 
  Installing       : gdbm-libs-1:1.23-4.fc39.s390x                       43/152 
  Installing       : libeconf-0.5.2-1.fc40.s390x                         44/152 
  Installing       : lz4-libs-1.9.4-4.fc39.s390x                         45/152 
  Installing       : mpfr-4.2.1-1.fc40.s390x                             46/152 
  Installing       : dwz-0.15-3.fc39.s390x                               47/152 
  Installing       : unzip-6.0-62.fc39.s390x                             48/152 
  Installing       : file-libs-5.45-1.fc40.s390x                         49/152 
  Installing       : file-5.45-1.fc40.s390x                              50/152 
  Installing       : alternatives-1.25-1.fc39.s390x                      51/152 
  Installing       : jansson-2.13.1-7.fc39.s390x                         52/152 
  Installing       : libcap-ng-0.8.3-8.fc40.s390x                        53/152 
  Installing       : audit-libs-3.1.2-5.fc40.s390x                       54/152 
  Installing       : pam-libs-1.5.3-8.fc40.s390x                         55/152 
  Installing       : libcap-2.69-1.fc40.s390x                            56/152 
  Installing       : systemd-libs-255-1.fc40.s390x                       57/152 
  Installing       : libcom_err-1.47.0-2.fc39.s390x                      58/152 
  Installing       : libsepol-3.6-0.rc2.1.fc40.s390x                     59/152 
  Installing       : libsmartcols-2.39.2-1.fc40.s390x                    60/152 
  Installing       : libtasn1-4.19.0-3.fc39.s390x                        61/152 
  Installing       : libunistring-1.1-5.fc40.s390x                       62/152 
  Installing       : libidn2-2.3.4-3.fc39.s390x                          63/152 
  Installing       : lua-libs-5.4.6-3.fc39.s390x                         64/152 
  Installing       : pcre2-10.42-2.fc40.s390x                            65/152 
  Installing       : libselinux-3.6-0.rc2.1.fc40.s390x                   66/152 
  Installing       : sed-4.8-14.fc39.s390x                               67/152 
  Installing       : grep-3.11-5.fc40.s390x                              68/152 
  Installing       : findutils-1:4.9.0-6.fc40.s390x                      69/152 
  Installing       : xz-5.4.5-1.fc40.s390x                               70/152 
  Installing       : libmount-2.39.2-1.fc40.s390x                        71/152 
  Installing       : util-linux-core-2.39.2-1.fc40.s390x                 72/152 
  Installing       : libsemanage-3.6-0.rc2.1.fc40.s390x                  73/152 
  Installing       : shadow-utils-2:4.14.0-2.fc40.s390x                  74/152 
  Running scriptlet: libutempter-1.2.1-10.fc39.s390x                     75/152 
  Installing       : libutempter-1.2.1-10.fc39.s390x                     75/152 
  Installing       : tar-2:1.35-2.fc40.s390x                             76/152 
  Installing       : libpsl-0.21.2-4.fc39.s390x                          77/152 
  Installing       : zip-3.0-39.fc40.s390x                               78/152 
  Installing       : zstd-1.5.5-4.fc39.s390x                             79/152 
  Installing       : cyrus-sasl-lib-2.1.28-11.fc39.s390x                 80/152 
  Installing       : gdbm-1:1.23-4.fc39.s390x                            81/152 
  Installing       : libfdisk-2.39.2-1.fc40.s390x                        82/152 
  Installing       : bzip2-1.0.8-16.fc39.s390x                           83/152 
  Installing       : libxml2-2.12.3-1.fc40.s390x                         84/152 
  Installing       : sqlite-libs-3.44.2-1.fc40.s390x                     85/152 
  Installing       : ed-1.19-4.fc39.s390x                                86/152 
  Installing       : patch-2.7.6-22.fc39.s390x                           87/152 
  Installing       : elfutils-default-yama-scope-0.190-4.fc40.noarch     88/152 
  Running scriptlet: elfutils-default-yama-scope-0.190-4.fc40.noarch     88/152 
  Installing       : cpio-2.14-5.fc40.s390x                              89/152 
  Installing       : diffutils-3.10-3.fc39.s390x                         90/152 
  Installing       : keyutils-libs-1.6.1-7.fc39.s390x                    91/152 
  Installing       : libbrotli-1.1.0-1.fc40.s390x                        92/152 
  Installing       : libffi-3.4.4-4.fc39.s390x                           93/152 
  Installing       : p11-kit-0.25.3-1.fc40.s390x                         94/152 
  Installing       : p11-kit-trust-0.25.3-1.fc40.s390x                   95/152 
  Running scriptlet: p11-kit-trust-0.25.3-1.fc40.s390x                   95/152 
  Installing       : libgomp-13.2.1-6.fc40.s390x                         96/152 
  Installing       : libnghttp2-1.58.0-1.fc40.s390x                      97/152 
  Installing       : libpkgconf-1.9.5-2.fc39.s390x                       98/152 
  Installing       : pkgconf-1.9.5-2.fc39.s390x                          99/152 
  Installing       : pkgconf-pkg-config-1.9.5-2.fc39.s390x              100/152 
  Installing       : libsigsegv-2.14-5.fc39.s390x                       101/152 
  Installing       : gawk-5.2.2-2.fc39.s390x                            102/152 
  Installing       : libverto-0.3.2-6.fc39.s390x                        103/152 
  Installing       : xxhash-libs-0.8.2-1.fc39.s390x                     104/152 
  Installing       : libssh-config-0.10.5-2.fc39.noarch                 105/152 
  Installing       : kernel-srpm-macros-1.0-20.fc39.noarch              106/152 
  Installing       : gnat-srpm-macros-6-3.fc39.noarch                   107/152 
  Installing       : ghc-srpm-macros-1.6.1-3.fc40.noarch                108/152 
  Installing       : fpc-srpm-macros-1.3-8.fc39.noarch                  109/152 
  Installing       : coreutils-common-9.4-1.fc40.s390x                  110/152 
  Installing       : openssl-libs-1:3.1.4-1.fc40.s390x                  111/152 
  Installing       : coreutils-9.4-1.fc40.s390x                         112/152 
  Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch   113/152 
  Installing       : ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch   113/152 
  Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch   113/152 
  Installing       : krb5-libs-1.21.2-2.fc40.s390x                      114/152 
  Installing       : libtirpc-1.3.4-0.fc40.s390x                        115/152 
  Running scriptlet: authselect-libs-1.4.3-1.fc40.s390x                 116/152 
  Installing       : authselect-libs-1.4.3-1.fc40.s390x                 116/152 
  Installing       : gzip-1.12-6.fc39.s390x                             117/152 
  Installing       : cracklib-2.9.11-2.fc39.s390x                       118/152 
  Installing       : libpwquality-1.4.5-6.fc39.s390x                    119/152 
  Installing       : authselect-1.4.3-1.fc40.s390x                      120/152 
  Installing       : libnsl2-2.0.0-6.fc39.s390x                         121/152 
  Installing       : pam-1.5.3-8.fc40.s390x                             122/152 
  Installing       : libssh-0.10.5-2.fc39.s390x                         123/152 
  Installing       : libarchive-3.7.2-1.fc40.s390x                      124/152 
  Installing       : libevent-2.1.12-9.fc39.s390x                       125/152 
  Installing       : openldap-2.6.6-1.fc39.s390x                        126/152 
  Installing       : libcurl-8.5.0-1.fc40.s390x                         127/152 
  Installing       : elfutils-libs-0.190-4.fc40.s390x                   128/152 
  Installing       : elfutils-debuginfod-client-0.190-4.fc40.s390x      129/152 
  Installing       : binutils-gold-2.41-16.fc40.s390x                   130/152 
  Running scriptlet: binutils-gold-2.41-16.fc40.s390x                   130/152 
  Installing       : binutils-2.41-16.fc40.s390x                        131/152 
  Running scriptlet: binutils-2.41-16.fc40.s390x                        131/152 
  Installing       : gdb-minimal-14.1-1.fc40.s390x                      132/152 
  Installing       : elfutils-0.190-4.fc40.s390x                        133/152 
  Installing       : debugedit-5.0-12.fc40.s390x                        134/152 
  Installing       : curl-8.5.0-1.fc40.s390x                            135/152 
  Installing       : rpm-sequoia-1.5.0-2.fc40.s390x                     136/152 
  Installing       : rpm-libs-4.19.1-1.fc40.s390x                       137/152 
  Running scriptlet: rpm-4.19.1-1.fc40.s390x                            138/152 
  Installing       : rpm-4.19.1-1.fc40.s390x                            138/152 
  Installing       : efi-srpm-macros-5-9.fc39.noarch                    139/152 
  Installing       : lua-srpm-macros-1-9.fc39.noarch                    140/152 
  Installing       : rpm-build-libs-4.19.1-1.fc40.s390x                 141/152 
  Installing       : ansible-srpm-macros-1-11.fc39.noarch               142/152 
  Installing       : fonts-srpm-macros-1:2.0.5-12.fc39.noarch           143/152 
  Installing       : forge-srpm-macros-0.2.0-1.fc40.noarch              144/152 
  Installing       : go-srpm-macros-3.3.1-1.fc40.noarch                 145/152 
  Installing       : python-srpm-macros-3.12-5.fc40.noarch              146/152 
  Installing       : redhat-rpm-config-271-1.fc40.noarch                147/152 
  Installing       : rpm-build-4.19.1-1.fc40.s390x                      148/152 
  Installing       : pyproject-srpm-macros-1.10.0-1.fc40.noarch         149/152 
  Installing       : util-linux-2.39.2-1.fc40.s390x                     150/152 
  Installing       : which-2.21-40.fc39.s390x                           151/152 
  Installing       : info-7.1-1.fc40.s390x                              152/152 
  Running scriptlet: filesystem-3.18-6.fc39.s390x                       152/152 
  Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch   152/152 
  Running scriptlet: authselect-libs-1.4.3-1.fc40.s390x                 152/152 
  Running scriptlet: rpm-4.19.1-1.fc40.s390x                            152/152 
  Running scriptlet: info-7.1-1.fc40.s390x                              152/152 

Installed:
  alternatives-1.25-1.fc39.s390x                                                
  ansible-srpm-macros-1-11.fc39.noarch                                          
  audit-libs-3.1.2-5.fc40.s390x                                                 
  authselect-1.4.3-1.fc40.s390x                                                 
  authselect-libs-1.4.3-1.fc40.s390x                                            
  basesystem-11-18.fc39.noarch                                                  
  bash-5.2.21-2.fc40.s390x                                                      
  binutils-2.41-16.fc40.s390x                                                   
  binutils-gold-2.41-16.fc40.s390x                                              
  bzip2-1.0.8-16.fc39.s390x                                                     
  bzip2-libs-1.0.8-16.fc39.s390x                                                
  ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch                              
  coreutils-9.4-1.fc40.s390x                                                    
  coreutils-common-9.4-1.fc40.s390x                                             
  cpio-2.14-5.fc40.s390x                                                        
  cracklib-2.9.11-2.fc39.s390x                                                  
  crypto-policies-20231204-1.git1e3a2e4.fc40.noarch                             
  curl-8.5.0-1.fc40.s390x                                                       
  cyrus-sasl-lib-2.1.28-11.fc39.s390x                                           
  debugedit-5.0-12.fc40.s390x                                                   
  diffutils-3.10-3.fc39.s390x                                                   
  dwz-0.15-3.fc39.s390x                                                         
  ed-1.19-4.fc39.s390x                                                          
  efi-srpm-macros-5-9.fc39.noarch                                               
  elfutils-0.190-4.fc40.s390x                                                   
  elfutils-debuginfod-client-0.190-4.fc40.s390x                                 
  elfutils-default-yama-scope-0.190-4.fc40.noarch                               
  elfutils-libelf-0.190-4.fc40.s390x                                            
  elfutils-libs-0.190-4.fc40.s390x                                              
  fedora-gpg-keys-40-0.2.noarch                                                 
  fedora-release-40-0.20.noarch                                                 
  fedora-release-common-40-0.20.noarch                                          
  fedora-release-identity-basic-40-0.20.noarch                                  
  fedora-repos-40-0.2.noarch                                                    
  fedora-repos-rawhide-40-0.2.noarch                                            
  file-5.45-1.fc40.s390x                                                        
  file-libs-5.45-1.fc40.s390x                                                   
  filesystem-3.18-6.fc39.s390x                                                  
  findutils-1:4.9.0-6.fc40.s390x                                                
  fonts-srpm-macros-1:2.0.5-12.fc39.noarch                                      
  forge-srpm-macros-0.2.0-1.fc40.noarch                                         
  fpc-srpm-macros-1.3-8.fc39.noarch                                             
  gawk-5.2.2-2.fc39.s390x                                                       
  gdb-minimal-14.1-1.fc40.s390x                                                 
  gdbm-1:1.23-4.fc39.s390x                                                      
  gdbm-libs-1:1.23-4.fc39.s390x                                                 
  ghc-srpm-macros-1.6.1-3.fc40.noarch                                           
  glibc-2.38.9000-27.fc40.s390x                                                 
  glibc-common-2.38.9000-27.fc40.s390x                                          
  glibc-gconv-extra-2.38.9000-27.fc40.s390x                                     
  glibc-minimal-langpack-2.38.9000-27.fc40.s390x                                
  gmp-1:6.2.1-5.fc39.s390x                                                      
  gnat-srpm-macros-6-3.fc39.noarch                                              
  go-srpm-macros-3.3.1-1.fc40.noarch                                            
  grep-3.11-5.fc40.s390x                                                        
  gzip-1.12-6.fc39.s390x                                                        
  info-7.1-1.fc40.s390x                                                         
  jansson-2.13.1-7.fc39.s390x                                                   
  kernel-srpm-macros-1.0-20.fc39.noarch                                         
  keyutils-libs-1.6.1-7.fc39.s390x                                              
  krb5-libs-1.21.2-2.fc40.s390x                                                 
  libacl-2.3.1-11.fc40.s390x                                                    
  libarchive-3.7.2-1.fc40.s390x                                                 
  libattr-2.5.1-9.fc40.s390x                                                    
  libblkid-2.39.2-1.fc40.s390x                                                  
  libbrotli-1.1.0-1.fc40.s390x                                                  
  libcap-2.69-1.fc40.s390x                                                      
  libcap-ng-0.8.3-8.fc40.s390x                                                  
  libcom_err-1.47.0-2.fc39.s390x                                                
  libcurl-8.5.0-1.fc40.s390x                                                    
  libeconf-0.5.2-1.fc40.s390x                                                   
  libevent-2.1.12-9.fc39.s390x                                                  
  libfdisk-2.39.2-1.fc40.s390x                                                  
  libffi-3.4.4-4.fc39.s390x                                                     
  libgcc-13.2.1-6.fc40.s390x                                                    
  libgomp-13.2.1-6.fc40.s390x                                                   
  libidn2-2.3.4-3.fc39.s390x                                                    
  libmount-2.39.2-1.fc40.s390x                                                  
  libnghttp2-1.58.0-1.fc40.s390x                                                
  libnsl2-2.0.0-6.fc39.s390x                                                    
  libpkgconf-1.9.5-2.fc39.s390x                                                 
  libpsl-0.21.2-4.fc39.s390x                                                    
  libpwquality-1.4.5-6.fc39.s390x                                               
  libselinux-3.6-0.rc2.1.fc40.s390x                                             
  libsemanage-3.6-0.rc2.1.fc40.s390x                                            
  libsepol-3.6-0.rc2.1.fc40.s390x                                               
  libsigsegv-2.14-5.fc39.s390x                                                  
  libsmartcols-2.39.2-1.fc40.s390x                                              
  libssh-0.10.5-2.fc39.s390x                                                    
  libssh-config-0.10.5-2.fc39.noarch                                            
  libstdc++-13.2.1-6.fc40.s390x                                                 
  libtasn1-4.19.0-3.fc39.s390x                                                  
  libtirpc-1.3.4-0.fc40.s390x                                                   
  libunistring-1.1-5.fc40.s390x                                                 
  libutempter-1.2.1-10.fc39.s390x                                               
  libuuid-2.39.2-1.fc40.s390x                                                   
  libverto-0.3.2-6.fc39.s390x                                                   
  libxcrypt-4.4.36-2.fc39.s390x                                                 
  libxml2-2.12.3-1.fc40.s390x                                                   
  libzstd-1.5.5-4.fc39.s390x                                                    
  lua-libs-5.4.6-3.fc39.s390x                                                   
  lua-srpm-macros-1-9.fc39.noarch                                               
  lz4-libs-1.9.4-4.fc39.s390x                                                   
  mpfr-4.2.1-1.fc40.s390x                                                       
  ncurses-base-6.4-8.20231001.fc40.noarch                                       
  ncurses-libs-6.4-8.20231001.fc40.s390x                                        
  ocaml-srpm-macros-9-1.fc40.noarch                                             
  openblas-srpm-macros-2-14.fc39.noarch                                         
  openldap-2.6.6-1.fc39.s390x                                                   
  openssl-libs-1:3.1.4-1.fc40.s390x                                             
  p11-kit-0.25.3-1.fc40.s390x                                                   
  p11-kit-trust-0.25.3-1.fc40.s390x                                             
  package-notes-srpm-macros-0.5-9.fc39.noarch                                   
  pam-1.5.3-8.fc40.s390x                                                        
  pam-libs-1.5.3-8.fc40.s390x                                                   
  patch-2.7.6-22.fc39.s390x                                                     
  pcre2-10.42-2.fc40.s390x                                                      
  pcre2-syntax-10.42-2.fc40.noarch                                              
  perl-srpm-macros-1-51.fc39.noarch                                             
  pkgconf-1.9.5-2.fc39.s390x                                                    
  pkgconf-m4-1.9.5-2.fc39.noarch                                                
  pkgconf-pkg-config-1.9.5-2.fc39.s390x                                         
  popt-1.19-3.fc39.s390x                                                        
  publicsuffix-list-dafsa-20230812-1.fc40.noarch                                
  pyproject-srpm-macros-1.10.0-1.fc40.noarch                                    
  python-srpm-macros-3.12-5.fc40.noarch                                         
  qt5-srpm-macros-5.15.11-1.fc40.noarch                                         
  qt6-srpm-macros-6.6.1-1.fc40.noarch                                           
  readline-8.2-4.fc39.s390x                                                     
  redhat-rpm-config-271-1.fc40.noarch                                           
  rpm-4.19.1-1.fc40.s390x                                                       
  rpm-build-4.19.1-1.fc40.s390x                                                 
  rpm-build-libs-4.19.1-1.fc40.s390x                                            
  rpm-libs-4.19.1-1.fc40.s390x                                                  
  rpm-sequoia-1.5.0-2.fc40.s390x                                                
  rust-srpm-macros-25.2-2.fc40.noarch                                           
  sed-4.8-14.fc39.s390x                                                         
  setup-2.14.5-1.fc40.noarch                                                    
  shadow-utils-2:4.14.0-2.fc40.s390x                                            
  sqlite-libs-3.44.2-1.fc40.s390x                                               
  systemd-libs-255-1.fc40.s390x                                                 
  tar-2:1.35-2.fc40.s390x                                                       
  unzip-6.0-62.fc39.s390x                                                       
  util-linux-2.39.2-1.fc40.s390x                                                
  util-linux-core-2.39.2-1.fc40.s390x                                           
  which-2.21-40.fc39.s390x                                                      
  xxhash-libs-0.8.2-1.fc39.s390x                                                
  xz-5.4.5-1.fc40.s390x                                                         
  xz-libs-5.4.5-1.fc40.s390x                                                    
  zip-3.0-39.fc40.s390x                                                         
  zlib-1.2.13-5.fc40.s390x                                                      
  zstd-1.5.5-4.fc39.s390x                                                       

Complete!
Finish: installing minimal buildroot with dnf
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: alternatives-1.25-1.fc39.s390x
ansible-srpm-macros-1-11.fc39.noarch
audit-libs-3.1.2-5.fc40.s390x
authselect-1.4.3-1.fc40.s390x
authselect-libs-1.4.3-1.fc40.s390x
basesystem-11-18.fc39.noarch
bash-5.2.21-2.fc40.s390x
binutils-2.41-16.fc40.s390x
binutils-gold-2.41-16.fc40.s390x
bzip2-1.0.8-16.fc39.s390x
bzip2-libs-1.0.8-16.fc39.s390x
ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch
coreutils-9.4-1.fc40.s390x
coreutils-common-9.4-1.fc40.s390x
cpio-2.14-5.fc40.s390x
cracklib-2.9.11-2.fc39.s390x
crypto-policies-20231204-1.git1e3a2e4.fc40.noarch
curl-8.5.0-1.fc40.s390x
cyrus-sasl-lib-2.1.28-11.fc39.s390x
debugedit-5.0-12.fc40.s390x
diffutils-3.10-3.fc39.s390x
dwz-0.15-3.fc39.s390x
ed-1.19-4.fc39.s390x
efi-srpm-macros-5-9.fc39.noarch
elfutils-0.190-4.fc40.s390x
elfutils-debuginfod-client-0.190-4.fc40.s390x
elfutils-default-yama-scope-0.190-4.fc40.noarch
elfutils-libelf-0.190-4.fc40.s390x
elfutils-libs-0.190-4.fc40.s390x
fedora-gpg-keys-40-0.2.noarch
fedora-release-40-0.20.noarch
fedora-release-common-40-0.20.noarch
fedora-release-identity-basic-40-0.20.noarch
fedora-repos-40-0.2.noarch
fedora-repos-rawhide-40-0.2.noarch
file-5.45-1.fc40.s390x
file-libs-5.45-1.fc40.s390x
filesystem-3.18-6.fc39.s390x
findutils-4.9.0-6.fc40.s390x
fonts-srpm-macros-2.0.5-12.fc39.noarch
forge-srpm-macros-0.2.0-1.fc40.noarch
fpc-srpm-macros-1.3-8.fc39.noarch
gawk-5.2.2-2.fc39.s390x
gdb-minimal-14.1-1.fc40.s390x
gdbm-1.23-4.fc39.s390x
gdbm-libs-1.23-4.fc39.s390x
ghc-srpm-macros-1.6.1-3.fc40.noarch
glibc-2.38.9000-27.fc40.s390x
glibc-common-2.38.9000-27.fc40.s390x
glibc-gconv-extra-2.38.9000-27.fc40.s390x
glibc-minimal-langpack-2.38.9000-27.fc40.s390x
gmp-6.2.1-5.fc39.s390x
gnat-srpm-macros-6-3.fc39.noarch
go-srpm-macros-3.3.1-1.fc40.noarch
gpg-pubkey-18b8e74c-62f2920f
gpg-pubkey-a15b79cc-63d04c2c
grep-3.11-5.fc40.s390x
gzip-1.12-6.fc39.s390x
info-7.1-1.fc40.s390x
jansson-2.13.1-7.fc39.s390x
kernel-srpm-macros-1.0-20.fc39.noarch
keyutils-libs-1.6.1-7.fc39.s390x
krb5-libs-1.21.2-2.fc40.s390x
libacl-2.3.1-11.fc40.s390x
libarchive-3.7.2-1.fc40.s390x
libattr-2.5.1-9.fc40.s390x
libblkid-2.39.2-1.fc40.s390x
libbrotli-1.1.0-1.fc40.s390x
libcap-2.69-1.fc40.s390x
libcap-ng-0.8.3-8.fc40.s390x
libcom_err-1.47.0-2.fc39.s390x
libcurl-8.5.0-1.fc40.s390x
libeconf-0.5.2-1.fc40.s390x
libevent-2.1.12-9.fc39.s390x
libfdisk-2.39.2-1.fc40.s390x
libffi-3.4.4-4.fc39.s390x
libgcc-13.2.1-6.fc40.s390x
libgomp-13.2.1-6.fc40.s390x
libidn2-2.3.4-3.fc39.s390x
libmount-2.39.2-1.fc40.s390x
libnghttp2-1.58.0-1.fc40.s390x
libnsl2-2.0.0-6.fc39.s390x
libpkgconf-1.9.5-2.fc39.s390x
libpsl-0.21.2-4.fc39.s390x
libpwquality-1.4.5-6.fc39.s390x
libselinux-3.6-0.rc2.1.fc40.s390x
libsemanage-3.6-0.rc2.1.fc40.s390x
libsepol-3.6-0.rc2.1.fc40.s390x
libsigsegv-2.14-5.fc39.s390x
libsmartcols-2.39.2-1.fc40.s390x
libssh-0.10.5-2.fc39.s390x
libssh-config-0.10.5-2.fc39.noarch
libstdc++-13.2.1-6.fc40.s390x
libtasn1-4.19.0-3.fc39.s390x
libtirpc-1.3.4-0.fc40.s390x
libunistring-1.1-5.fc40.s390x
libutempter-1.2.1-10.fc39.s390x
libuuid-2.39.2-1.fc40.s390x
libverto-0.3.2-6.fc39.s390x
libxcrypt-4.4.36-2.fc39.s390x
libxml2-2.12.3-1.fc40.s390x
libzstd-1.5.5-4.fc39.s390x
lua-libs-5.4.6-3.fc39.s390x
lua-srpm-macros-1-9.fc39.noarch
lz4-libs-1.9.4-4.fc39.s390x
mpfr-4.2.1-1.fc40.s390x
ncurses-base-6.4-8.20231001.fc40.noarch
ncurses-libs-6.4-8.20231001.fc40.s390x
ocaml-srpm-macros-9-1.fc40.noarch
openblas-srpm-macros-2-14.fc39.noarch
openldap-2.6.6-1.fc39.s390x
openssl-libs-3.1.4-1.fc40.s390x
p11-kit-0.25.3-1.fc40.s390x
p11-kit-trust-0.25.3-1.fc40.s390x
package-notes-srpm-macros-0.5-9.fc39.noarch
pam-1.5.3-8.fc40.s390x
pam-libs-1.5.3-8.fc40.s390x
patch-2.7.6-22.fc39.s390x
pcre2-10.42-2.fc40.s390x
pcre2-syntax-10.42-2.fc40.noarch
perl-srpm-macros-1-51.fc39.noarch
pkgconf-1.9.5-2.fc39.s390x
pkgconf-m4-1.9.5-2.fc39.noarch
pkgconf-pkg-config-1.9.5-2.fc39.s390x
popt-1.19-3.fc39.s390x
publicsuffix-list-dafsa-20230812-1.fc40.noarch
pyproject-srpm-macros-1.10.0-1.fc40.noarch
python-srpm-macros-3.12-5.fc40.noarch
qt5-srpm-macros-5.15.11-1.fc40.noarch
qt6-srpm-macros-6.6.1-1.fc40.noarch
readline-8.2-4.fc39.s390x
redhat-rpm-config-271-1.fc40.noarch
rpm-4.19.1-1.fc40.s390x
rpm-build-4.19.1-1.fc40.s390x
rpm-build-libs-4.19.1-1.fc40.s390x
rpm-libs-4.19.1-1.fc40.s390x
rpm-sequoia-1.5.0-2.fc40.s390x
rust-srpm-macros-25.2-2.fc40.noarch
sed-4.8-14.fc39.s390x
setup-2.14.5-1.fc40.noarch
shadow-utils-4.14.0-2.fc40.s390x
sqlite-libs-3.44.2-1.fc40.s390x
systemd-libs-255-1.fc40.s390x
tar-1.35-2.fc40.s390x
unzip-6.0-62.fc39.s390x
util-linux-2.39.2-1.fc40.s390x
util-linux-core-2.39.2-1.fc40.s390x
which-2.21-40.fc39.s390x
xxhash-libs-0.8.2-1.fc39.s390x
xz-5.4.5-1.fc40.s390x
xz-libs-5.4.5-1.fc40.s390x
zip-3.0-39.fc40.s390x
zlib-1.2.13-5.fc40.s390x
zstd-1.5.5-4.fc39.s390x
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1701993600
Wrote: /builddir/build/SRPMS/percolator-3.06.04-1.fc40.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-s390x-1702546936.417971/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-s390x-1702546936.417971/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-s390x-1702546936.417971/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-bg5dzm32/percolator/percolator.spec) Config(child) 2 minutes 2 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/percolator-3.06.04-1.fc40.src.rpm)  Config(fedora-rawhide-s390x)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1702546936.417971/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1702546936.417971/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-1702546936.417971/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Finish: chroot init
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.1-1.fc40.s390x
  rpm-sequoia-1.5.0-2.fc40.s390x
  python3-dnf-4.18.2-1.fc40.noarch
  python3-dnf-plugins-core-4.4.4-1.fc40.noarch
  yum-4.18.2-1.fc40.noarch
Start: build phase for percolator-3.06.04-1.fc40.src.rpm
Start: build setup for percolator-3.06.04-1.fc40.src.rpm
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1701993600
Wrote: /builddir/build/SRPMS/percolator-3.06.04-1.fc40.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                 232  B/s | 1.5 kB     00:06    
fedora                                           52 kB/s | 5.6 kB     00:00    
Dependencies resolved.
================================================================================
 Package                     Arch     Version                 Repository   Size
================================================================================
Installing:
 boost-devel                 s390x    1.83.0-0.fc40           copr_base    12 M
 boost-static                s390x    1.83.0-0.fc40           copr_base   3.3 M
 bzip2-devel                 s390x    1.0.8-16.fc39           fedora      214 k
 cmake                       s390x    3.27.7-1.fc40           fedora      7.8 M
 gcc                         s390x    13.2.1-6.fc40           fedora       28 M
 gcc-c++                     s390x    13.2.1-6.fc40           fedora       11 M
 gtest-devel                 s390x    1.14.0-2.fc40           fedora      255 k
 libtirpc-devel              s390x    1.3.4-0.fc40            fedora      125 k
 make                        s390x    1:4.4.1-2.fc39          fedora      605 k
 python3-devel               s390x    3.12.1-1.fc40           fedora      312 k
 sqlite-devel                s390x    3.44.2-1.fc40           fedora      148 k
 tokyocabinet-devel          s390x    1.4.48-23.fc39          fedora       93 k
 xerces-c-devel              s390x    3.2.3-9.fc39            fedora      509 k
 xsd                         s390x    4.1.0-0.12.a11.fc40     copr_base   1.2 M
 zlib-devel                  s390x    1.2.13-5.fc40           fedora       44 k
Installing dependencies:
 annobin-docs                noarch   12.33-1.fc40            fedora       91 k
 annobin-plugin-gcc          s390x    12.33-1.fc40            fedora      958 k
 boost                       s390x    1.83.0-0.fc40           copr_base    14 k
 boost-atomic                s390x    1.83.0-0.fc40           copr_base    19 k
 boost-chrono                s390x    1.83.0-0.fc40           copr_base    26 k
 boost-container             s390x    1.83.0-0.fc40           copr_base    41 k
 boost-context               s390x    1.83.0-0.fc40           copr_base    17 k
 boost-contract              s390x    1.83.0-0.fc40           copr_base    45 k
 boost-coroutine             s390x    1.83.0-0.fc40           copr_base    21 k
 boost-date-time             s390x    1.83.0-0.fc40           copr_base    16 k
 boost-fiber                 s390x    1.83.0-0.fc40           copr_base    43 k
 boost-filesystem            s390x    1.83.0-0.fc40           copr_base    68 k
 boost-graph                 s390x    1.83.0-0.fc40           copr_base   159 k
 boost-iostreams             s390x    1.83.0-0.fc40           copr_base    41 k
 boost-json                  s390x    1.83.0-0.fc40           copr_base   154 k
 boost-locale                s390x    1.83.0-0.fc40           copr_base   215 k
 boost-log                   s390x    1.83.0-0.fc40           copr_base   498 k
 boost-math                  s390x    1.83.0-0.fc40           copr_base   238 k
 boost-nowide                s390x    1.83.0-0.fc40           copr_base    21 k
 boost-numpy3                s390x    1.83.0-0.fc40           copr_base    30 k
 boost-program-options       s390x    1.83.0-0.fc40           copr_base   111 k
 boost-python3               s390x    1.83.0-0.fc40           copr_base    95 k
 boost-random                s390x    1.83.0-0.fc40           copr_base    24 k
 boost-regex                 s390x    1.83.0-0.fc40           copr_base   123 k
 boost-serialization         s390x    1.83.0-0.fc40           copr_base   136 k
 boost-stacktrace            s390x    1.83.0-0.fc40           copr_base    30 k
 boost-system                s390x    1.83.0-0.fc40           copr_base    16 k
 boost-test                  s390x    1.83.0-0.fc40           copr_base   250 k
 boost-thread                s390x    1.83.0-0.fc40           copr_base    62 k
 boost-timer                 s390x    1.83.0-0.fc40           copr_base    22 k
 boost-type_erasure          s390x    1.83.0-0.fc40           copr_base    33 k
 boost-wave                  s390x    1.83.0-0.fc40           copr_base   245 k
 cmake-data                  noarch   3.27.7-1.fc40           fedora      2.2 M
 cmake-filesystem            s390x    3.27.7-1.fc40           fedora       19 k
 cmake-rpm-macros            noarch   3.27.7-1.fc40           fedora       19 k
 cpp                         s390x    13.2.1-6.fc40           fedora      8.8 M
 emacs-filesystem            noarch   1:29.1-14.fc40          fedora      7.4 k
 expat                       s390x    2.5.0-3.fc39            fedora      114 k
 flexiblas                   s390x    3.3.1-5.fc39            fedora       33 k
 flexiblas-netlib            s390x    3.3.1-5.fc39            fedora      3.6 M
 flexiblas-openblas-openmp   s390x    3.3.1-5.fc39            fedora       17 k
 gc                          s390x    8.2.2-4.fc39            fedora      114 k
 gcc-plugin-annobin          s390x    13.2.1-6.fc40           fedora       49 k
 glibc-devel                 s390x    2.38.9000-27.fc40       fedora      110 k
 glibc-headers-s390          noarch   2.38.9000-27.fc40       fedora      578 k
 gmock                       s390x    1.14.0-2.fc40           fedora       58 k
 gtest                       s390x    1.14.0-2.fc40           fedora      173 k
 guile22                     s390x    2.2.7-9.fc39            fedora      6.5 M
 jsoncpp                     s390x    1.9.5-5.fc39            fedora       96 k
 kernel-headers              s390x    6.7.0-0.rc5.41.fc40     fedora      1.6 M
 libasan                     s390x    13.2.1-6.fc40           fedora      510 k
 libatomic                   s390x    13.2.1-6.fc40           fedora       37 k
 libb2                       s390x    0.98.1-9.fc39           fedora       27 k
 libcutl                     s390x    1.10.0-27.fc39          fedora      326 k
 libgfortran                 s390x    13.2.1-6.fc40           fedora      580 k
 libicu                      s390x    73.2-2.fc39             fedora       11 M
 libicu-devel                s390x    73.2-2.fc39             fedora      925 k
 libmpc                      s390x    1.3.1-3.fc39            fedora       73 k
 libstdc++-devel             s390x    13.2.1-6.fc40           fedora      2.6 M
 libtool-ltdl                s390x    2.4.7-8.fc40            fedora       37 k
 libubsan                    s390x    13.2.1-6.fc40           fedora      222 k
 libuv                       s390x    1:1.47.0-3.fc40         fedora      252 k
 libxcrypt-devel             s390x    4.4.36-2.fc39           fedora       30 k
 mpdecimal                   s390x    2.5.1-7.fc39            fedora      100 k
 openblas                    s390x    0.3.25-1.fc40           fedora       38 k
 openblas-openmp             s390x    0.3.25-1.fc40           fedora      4.3 M
 pyproject-rpm-macros        noarch   1.10.0-1.fc40           fedora       41 k
 python-pip-wheel            noarch   23.2.1-1.fc39           fedora      1.5 M
 python-rpm-macros           noarch   3.12-5.fc40             fedora       19 k
 python3                     s390x    3.12.1-1.fc40           fedora       26 k
 python3-libs                s390x    3.12.1-1.fc40           fedora      9.2 M
 python3-numpy               s390x    1:1.26.0-2.fc40         fedora      7.1 M
 python3-packaging           noarch   23.2-2.fc40             fedora      125 k
 python3-rpm-generators      noarch   14-8.fc40               fedora       30 k
 python3-rpm-macros          noarch   3.12-5.fc40             fedora       14 k
 rhash                       s390x    1.4.3-3.fc39            fedora      200 k
 sqlite                      s390x    3.44.2-1.fc40           fedora      901 k
 tokyocabinet                s390x    1.4.48-23.fc39          fedora      546 k
 tzdata                      noarch   2023c-4.fc40            fedora      717 k
 vim-filesystem              noarch   2:9.0.2153-1.fc40       fedora       18 k
 xerces-c                    s390x    3.2.3-9.fc39            fedora      963 k

Transaction Summary
================================================================================
Install  96 Packages

Total download size: 135 M
Installed size: 596 M
Downloading Packages:
(1/96): boost-chrono-1.83.0-0.fc40.s390x.rpm     77 kB/s |  26 kB     00:00    
(2/96): boost-1.83.0-0.fc40.s390x.rpm            43 kB/s |  14 kB     00:00    
(3/96): boost-atomic-1.83.0-0.fc40.s390x.rpm     56 kB/s |  19 kB     00:00    
(4/96): boost-container-1.83.0-0.fc40.s390x.rpm 315 kB/s |  41 kB     00:00    
(5/96): boost-context-1.83.0-0.fc40.s390x.rpm    91 kB/s |  17 kB     00:00    
(6/96): boost-contract-1.83.0-0.fc40.s390x.rpm  202 kB/s |  45 kB     00:00    
(7/96): boost-coroutine-1.83.0-0.fc40.s390x.rpm 168 kB/s |  21 kB     00:00    
(8/96): boost-date-time-1.83.0-0.fc40.s390x.rpm 157 kB/s |  16 kB     00:00    
(9/96): boost-fiber-1.83.0-0.fc40.s390x.rpm     114 kB/s |  43 kB     00:00    
(10/96): boost-filesystem-1.83.0-0.fc40.s390x.r 198 kB/s |  68 kB     00:00    
(11/96): boost-graph-1.83.0-0.fc40.s390x.rpm    725 kB/s | 159 kB     00:00    
(12/96): boost-iostreams-1.83.0-0.fc40.s390x.rp 189 kB/s |  41 kB     00:00    
(13/96): boost-devel-1.83.0-0.fc40.s390x.rpm     15 MB/s |  12 MB     00:00    
(14/96): boost-json-1.83.0-0.fc40.s390x.rpm     810 kB/s | 154 kB     00:00    
(15/96): boost-locale-1.83.0-0.fc40.s390x.rpm   1.1 MB/s | 215 kB     00:00    
(16/96): boost-math-1.83.0-0.fc40.s390x.rpm     2.3 MB/s | 238 kB     00:00    
(17/96): boost-log-1.83.0-0.fc40.s390x.rpm      4.8 MB/s | 498 kB     00:00    
(18/96): boost-nowide-1.83.0-0.fc40.s390x.rpm   216 kB/s |  21 kB     00:00    
(19/96): boost-numpy3-1.83.0-0.fc40.s390x.rpm   314 kB/s |  30 kB     00:00    
(20/96): boost-program-options-1.83.0-0.fc40.s3 1.1 MB/s | 111 kB     00:00    
(21/96): boost-python3-1.83.0-0.fc40.s390x.rpm  986 kB/s |  95 kB     00:00    
(22/96): boost-random-1.83.0-0.fc40.s390x.rpm   260 kB/s |  24 kB     00:00    
(23/96): boost-regex-1.83.0-0.fc40.s390x.rpm    1.3 MB/s | 123 kB     00:00    
(24/96): boost-serialization-1.83.0-0.fc40.s390 1.4 MB/s | 136 kB     00:00    
(25/96): boost-stacktrace-1.83.0-0.fc40.s390x.r 322 kB/s |  30 kB     00:00    
(26/96): boost-system-1.83.0-0.fc40.s390x.rpm   171 kB/s |  16 kB     00:00    
(27/96): boost-test-1.83.0-0.fc40.s390x.rpm     2.5 MB/s | 250 kB     00:00    
(28/96): boost-thread-1.83.0-0.fc40.s390x.rpm   659 kB/s |  62 kB     00:00    
(29/96): boost-timer-1.83.0-0.fc40.s390x.rpm    233 kB/s |  22 kB     00:00    
(30/96): boost-type_erasure-1.83.0-0.fc40.s390x 351 kB/s |  33 kB     00:00    
(31/96): boost-wave-1.83.0-0.fc40.s390x.rpm     2.5 MB/s | 245 kB     00:00    
(32/96): annobin-docs-12.33-1.fc40.noarch.rpm   797 kB/s |  91 kB     00:00    
(33/96): annobin-plugin-gcc-12.33-1.fc40.s390x.  10 MB/s | 958 kB     00:00    
(34/96): bzip2-devel-1.0.8-16.fc39.s390x.rpm    6.6 MB/s | 214 kB     00:00    
(35/96): cmake-3.27.7-1.fc40.s390x.rpm           60 MB/s | 7.8 MB     00:00    
(36/96): cmake-data-3.27.7-1.fc40.noarch.rpm     42 MB/s | 2.2 MB     00:00    
(37/96): cmake-filesystem-3.27.7-1.fc40.s390x.r 612 kB/s |  19 kB     00:00    
(38/96): cmake-rpm-macros-3.27.7-1.fc40.noarch. 615 kB/s |  19 kB     00:00    
(39/96): cpp-13.2.1-6.fc40.s390x.rpm             69 MB/s | 8.8 MB     00:00    
(40/96): emacs-filesystem-29.1-14.fc40.noarch.r 211 kB/s | 7.4 kB     00:00    
(41/96): boost-static-1.83.0-0.fc40.s390x.rpm   3.2 MB/s | 3.3 MB     00:01    
(42/96): expat-2.5.0-3.fc39.s390x.rpm           4.4 MB/s | 114 kB     00:00    
(43/96): flexiblas-3.3.1-5.fc39.s390x.rpm       524 kB/s |  33 kB     00:00    
(44/96): flexiblas-netlib-3.3.1-5.fc39.s390x.rp  51 MB/s | 3.6 MB     00:00    
(45/96): flexiblas-openblas-openmp-3.3.1-5.fc39 436 kB/s |  17 kB     00:00    
(46/96): gc-8.2.2-4.fc39.s390x.rpm              3.1 MB/s | 114 kB     00:00    
(47/96): xsd-4.1.0-0.12.a11.fc40.s390x.rpm      1.3 MB/s | 1.2 MB     00:00    
(48/96): gcc-plugin-annobin-13.2.1-6.fc40.s390x 562 kB/s |  49 kB     00:00    
(49/96): gcc-c++-13.2.1-6.fc40.s390x.rpm         65 MB/s |  11 MB     00:00    
(50/96): glibc-headers-s390-2.38.9000-27.fc40.n  15 MB/s | 578 kB     00:00    
(51/96): glibc-devel-2.38.9000-27.fc40.s390x.rp 1.8 MB/s | 110 kB     00:00    
(52/96): gmock-1.14.0-2.fc40.s390x.rpm          1.5 MB/s |  58 kB     00:00    
(53/96): gtest-1.14.0-2.fc40.s390x.rpm          4.4 MB/s | 173 kB     00:00    
(54/96): gtest-devel-1.14.0-2.fc40.s390x.rpm    6.5 MB/s | 255 kB     00:00    
(55/96): gcc-13.2.1-6.fc40.s390x.rpm             84 MB/s |  28 MB     00:00    
(56/96): jsoncpp-1.9.5-5.fc39.s390x.rpm         2.6 MB/s |  96 kB     00:00    
(57/96): libasan-13.2.1-6.fc40.s390x.rpm         15 MB/s | 510 kB     00:00    
(58/96): kernel-headers-6.7.0-0.rc5.41.fc40.s39  32 MB/s | 1.6 MB     00:00    
(59/96): libatomic-13.2.1-6.fc40.s390x.rpm      1.0 MB/s |  37 kB     00:00    
(60/96): libb2-0.98.1-9.fc39.s390x.rpm          856 kB/s |  27 kB     00:00    
(61/96): guile22-2.2.7-9.fc39.s390x.rpm          42 MB/s | 6.5 MB     00:00    
(62/96): libgfortran-13.2.1-6.fc40.s390x.rpm     13 MB/s | 580 kB     00:00    
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(65/96): libmpc-1.3.1-3.fc39.s390x.rpm          2.0 MB/s |  73 kB     00:00    
(66/96): libtirpc-devel-1.3.4-0.fc40.s390x.rpm  7.9 MB/s | 125 kB     00:00    
(67/96): libstdc++-devel-13.2.1-6.fc40.s390x.rp  49 MB/s | 2.6 MB     00:00    
(68/96): libtool-ltdl-2.4.7-8.fc40.s390x.rpm    1.1 MB/s |  37 kB     00:00    
(69/96): libubsan-13.2.1-6.fc40.s390x.rpm       9.7 MB/s | 222 kB     00:00    
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(71/96): libicu-73.2-2.fc39.s390x.rpm            57 MB/s |  11 MB     00:00    
(72/96): libxcrypt-devel-4.4.36-2.fc39.s390x.rp 769 kB/s |  30 kB     00:00    
(73/96): make-4.4.1-2.fc39.s390x.rpm             15 MB/s | 605 kB     00:00    
(74/96): mpdecimal-2.5.1-7.fc39.s390x.rpm       3.9 MB/s | 100 kB     00:00    
(75/96): openblas-0.3.25-1.fc40.s390x.rpm       1.0 MB/s |  38 kB     00:00    
(76/96): pyproject-rpm-macros-1.10.0-1.fc40.noa 1.8 MB/s |  41 kB     00:00    
(77/96): python-pip-wheel-23.2.1-1.fc39.noarch.  39 MB/s | 1.5 MB     00:00    
(78/96): python-rpm-macros-3.12-5.fc40.noarch.r 599 kB/s |  19 kB     00:00    
(79/96): openblas-openmp-0.3.25-1.fc40.s390x.rp  45 MB/s | 4.3 MB     00:00    
(80/96): python3-devel-3.12.1-1.fc40.s390x.rpm  7.4 MB/s | 312 kB     00:00    
(81/96): python3-3.12.1-1.fc40.s390x.rpm        515 kB/s |  26 kB     00:00    
(82/96): python3-packaging-23.2-2.fc40.noarch.r 7.7 MB/s | 125 kB     00:00    
(83/96): python3-rpm-generators-14-8.fc40.noarc 1.0 MB/s |  30 kB     00:00    
(84/96): python3-rpm-macros-3.12-5.fc40.noarch. 329 kB/s |  14 kB     00:00    
(85/96): python3-numpy-1.26.0-2.fc40.s390x.rpm   59 MB/s | 7.1 MB     00:00    
(86/96): rhash-1.4.3-3.fc39.s390x.rpm           5.2 MB/s | 200 kB     00:00    
(87/96): python3-libs-3.12.1-1.fc40.s390x.rpm    60 MB/s | 9.2 MB     00:00    
(88/96): sqlite-3.44.2-1.fc40.s390x.rpm          24 MB/s | 901 kB     00:00    
(89/96): sqlite-devel-3.44.2-1.fc40.s390x.rpm   4.9 MB/s | 148 kB     00:00    
(90/96): tokyocabinet-1.4.48-23.fc39.s390x.rpm   18 MB/s | 546 kB     00:00    
(91/96): tzdata-2023c-4.fc40.noarch.rpm          20 MB/s | 717 kB     00:00    
(92/96): tokyocabinet-devel-1.4.48-23.fc39.s390 2.4 MB/s |  93 kB     00:00    
(93/96): vim-filesystem-9.0.2153-1.fc40.noarch. 482 kB/s |  18 kB     00:00    
(94/96): xerces-c-3.2.3-9.fc39.s390x.rpm         26 MB/s | 963 kB     00:00    
(95/96): xerces-c-devel-3.2.3-9.fc39.s390x.rpm   13 MB/s | 509 kB     00:00    
(96/96): zlib-devel-1.2.13-5.fc40.s390x.rpm     1.3 MB/s |  44 kB     00:00    
--------------------------------------------------------------------------------
Total                                            35 MB/s | 135 MB     00:03     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
  Installing       : boost-system-1.83.0-0.fc40.s390x                      1/96 
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  Installing       : boost-thread-1.83.0-0.fc40.s390x                      3/96 
  Installing       : libicu-73.2-2.fc39.s390x                              4/96 
  Installing       : boost-regex-1.83.0-0.fc40.s390x                       5/96 
  Installing       : python-rpm-macros-3.12-5.fc40.noarch                  6/96 
  Installing       : libmpc-1.3.1-3.fc39.s390x                             7/96 
  Installing       : expat-2.5.0-3.fc39.s390x                              8/96 
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  Installing       : boost-context-1.83.0-0.fc40.s390x                    10/96 
  Installing       : boost-atomic-1.83.0-0.fc40.s390x                     11/96 
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  Installing       : xerces-c-3.2.3-9.fc39.s390x                          14/96 
  Installing       : libgfortran-13.2.1-6.fc40.s390x                      15/96 
  Installing       : gtest-1.14.0-2.fc40.s390x                            16/96 
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  Installing       : libcutl-1.10.0-27.fc39.s390x                         26/96 
  Installing       : cpp-13.2.1-6.fc40.s390x                              27/96 
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  Installing       : boost-locale-1.83.0-0.fc40.s390x                     29/96 
  Installing       : libicu-devel-73.2-2.fc39.s390x                       30/96 
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  Installing       : vim-filesystem-2:9.0.2153-1.fc40.noarch              33/96 
  Installing       : tzdata-2023c-4.fc40.noarch                           34/96 
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  Installing       : sqlite-3.44.2-1.fc40.s390x                           36/96 
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  Installing       : openblas-0.3.25-1.fc40.s390x                         39/96 
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  Installing       : flexiblas-netlib-3.3.1-5.fc39.s390x                  41/96 
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  Installing       : flexiblas-3.3.1-5.fc39.s390x                         43/96 
  Installing       : mpdecimal-2.5.1-7.fc39.s390x                         44/96 
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  Installing       : make-1:4.4.1-2.fc39.s390x                            67/96 
  Installing       : gcc-13.2.1-6.fc40.s390x                              68/96 
  Running scriptlet: gcc-13.2.1-6.fc40.s390x                              68/96 
  Installing       : emacs-filesystem-1:29.1-14.fc40.noarch               69/96 
  Installing       : cmake-data-3.27.7-1.fc40.noarch                      70/96 
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  Installing       : annobin-docs-12.33-1.fc40.noarch                     72/96 
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  Installing       : boost-1.83.0-0.fc40.s390x                            82/96 
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  Installing       : boost-static-1.83.0-0.fc40.s390x                     84/96 
  Installing       : annobin-plugin-gcc-12.33-1.fc40.s390x                85/96 
  Running scriptlet: annobin-plugin-gcc-12.33-1.fc40.s390x                85/96 
  Installing       : gcc-c++-13.2.1-6.fc40.s390x                          86/96 
  Installing       : gcc-plugin-annobin-13.2.1-6.fc40.s390x               87/96 
  Running scriptlet: gcc-plugin-annobin-13.2.1-6.fc40.s390x               87/96 
  Installing       : python3-devel-3.12.1-1.fc40.s390x                    88/96 
  Installing       : sqlite-devel-3.44.2-1.fc40.s390x                     89/96 
  Installing       : tokyocabinet-devel-1.4.48-23.fc39.s390x              90/96 
  Installing       : xsd-4.1.0-0.12.a11.fc40.s390x                        91/96 
  Installing       : gtest-devel-1.14.0-2.fc40.s390x                      92/96 
  Installing       : xerces-c-devel-3.2.3-9.fc39.s390x                    93/96 
  Installing       : zlib-devel-1.2.13-5.fc40.s390x                       94/96 
  Installing       : libtirpc-devel-1.3.4-0.fc40.s390x                    95/96 
  Installing       : bzip2-devel-1.0.8-16.fc39.s390x                      96/96 
  Running scriptlet: bzip2-devel-1.0.8-16.fc39.s390x                      96/96 

Installed:
  annobin-docs-12.33-1.fc40.noarch                                              
  annobin-plugin-gcc-12.33-1.fc40.s390x                                         
  boost-1.83.0-0.fc40.s390x                                                     
  boost-atomic-1.83.0-0.fc40.s390x                                              
  boost-chrono-1.83.0-0.fc40.s390x                                              
  boost-container-1.83.0-0.fc40.s390x                                           
  boost-context-1.83.0-0.fc40.s390x                                             
  boost-contract-1.83.0-0.fc40.s390x                                            
  boost-coroutine-1.83.0-0.fc40.s390x                                           
  boost-date-time-1.83.0-0.fc40.s390x                                           
  boost-devel-1.83.0-0.fc40.s390x                                               
  boost-fiber-1.83.0-0.fc40.s390x                                               
  boost-filesystem-1.83.0-0.fc40.s390x                                          
  boost-graph-1.83.0-0.fc40.s390x                                               
  boost-iostreams-1.83.0-0.fc40.s390x                                           
  boost-json-1.83.0-0.fc40.s390x                                                
  boost-locale-1.83.0-0.fc40.s390x                                              
  boost-log-1.83.0-0.fc40.s390x                                                 
  boost-math-1.83.0-0.fc40.s390x                                                
  boost-nowide-1.83.0-0.fc40.s390x                                              
  boost-numpy3-1.83.0-0.fc40.s390x                                              
  boost-program-options-1.83.0-0.fc40.s390x                                     
  boost-python3-1.83.0-0.fc40.s390x                                             
  boost-random-1.83.0-0.fc40.s390x                                              
  boost-regex-1.83.0-0.fc40.s390x                                               
  boost-serialization-1.83.0-0.fc40.s390x                                       
  boost-stacktrace-1.83.0-0.fc40.s390x                                          
  boost-static-1.83.0-0.fc40.s390x                                              
  boost-system-1.83.0-0.fc40.s390x                                              
  boost-test-1.83.0-0.fc40.s390x                                                
  boost-thread-1.83.0-0.fc40.s390x                                              
  boost-timer-1.83.0-0.fc40.s390x                                               
  boost-type_erasure-1.83.0-0.fc40.s390x                                        
  boost-wave-1.83.0-0.fc40.s390x                                                
  bzip2-devel-1.0.8-16.fc39.s390x                                               
  cmake-3.27.7-1.fc40.s390x                                                     
  cmake-data-3.27.7-1.fc40.noarch                                               
  cmake-filesystem-3.27.7-1.fc40.s390x                                          
  cmake-rpm-macros-3.27.7-1.fc40.noarch                                         
  cpp-13.2.1-6.fc40.s390x                                                       
  emacs-filesystem-1:29.1-14.fc40.noarch                                        
  expat-2.5.0-3.fc39.s390x                                                      
  flexiblas-3.3.1-5.fc39.s390x                                                  
  flexiblas-netlib-3.3.1-5.fc39.s390x                                           
  flexiblas-openblas-openmp-3.3.1-5.fc39.s390x                                  
  gc-8.2.2-4.fc39.s390x                                                         
  gcc-13.2.1-6.fc40.s390x                                                       
  gcc-c++-13.2.1-6.fc40.s390x                                                   
  gcc-plugin-annobin-13.2.1-6.fc40.s390x                                        
  glibc-devel-2.38.9000-27.fc40.s390x                                           
  glibc-headers-s390-2.38.9000-27.fc40.noarch                                   
  gmock-1.14.0-2.fc40.s390x                                                     
  gtest-1.14.0-2.fc40.s390x                                                     
  gtest-devel-1.14.0-2.fc40.s390x                                               
  guile22-2.2.7-9.fc39.s390x                                                    
  jsoncpp-1.9.5-5.fc39.s390x                                                    
  kernel-headers-6.7.0-0.rc5.41.fc40.s390x                                      
  libasan-13.2.1-6.fc40.s390x                                                   
  libatomic-13.2.1-6.fc40.s390x                                                 
  libb2-0.98.1-9.fc39.s390x                                                     
  libcutl-1.10.0-27.fc39.s390x                                                  
  libgfortran-13.2.1-6.fc40.s390x                                               
  libicu-73.2-2.fc39.s390x                                                      
  libicu-devel-73.2-2.fc39.s390x                                                
  libmpc-1.3.1-3.fc39.s390x                                                     
  libstdc++-devel-13.2.1-6.fc40.s390x                                           
  libtirpc-devel-1.3.4-0.fc40.s390x                                             
  libtool-ltdl-2.4.7-8.fc40.s390x                                               
  libubsan-13.2.1-6.fc40.s390x                                                  
  libuv-1:1.47.0-3.fc40.s390x                                                   
  libxcrypt-devel-4.4.36-2.fc39.s390x                                           
  make-1:4.4.1-2.fc39.s390x                                                     
  mpdecimal-2.5.1-7.fc39.s390x                                                  
  openblas-0.3.25-1.fc40.s390x                                                  
  openblas-openmp-0.3.25-1.fc40.s390x                                           
  pyproject-rpm-macros-1.10.0-1.fc40.noarch                                     
  python-pip-wheel-23.2.1-1.fc39.noarch                                         
  python-rpm-macros-3.12-5.fc40.noarch                                          
  python3-3.12.1-1.fc40.s390x                                                   
  python3-devel-3.12.1-1.fc40.s390x                                             
  python3-libs-3.12.1-1.fc40.s390x                                              
  python3-numpy-1:1.26.0-2.fc40.s390x                                           
  python3-packaging-23.2-2.fc40.noarch                                          
  python3-rpm-generators-14-8.fc40.noarch                                       
  python3-rpm-macros-3.12-5.fc40.noarch                                         
  rhash-1.4.3-3.fc39.s390x                                                      
  sqlite-3.44.2-1.fc40.s390x                                                    
  sqlite-devel-3.44.2-1.fc40.s390x                                              
  tokyocabinet-1.4.48-23.fc39.s390x                                             
  tokyocabinet-devel-1.4.48-23.fc39.s390x                                       
  tzdata-2023c-4.fc40.noarch                                                    
  vim-filesystem-2:9.0.2153-1.fc40.noarch                                       
  xerces-c-3.2.3-9.fc39.s390x                                                   
  xerces-c-devel-3.2.3-9.fc39.s390x                                             
  xsd-4.1.0-0.12.a11.fc40.s390x                                                 
  zlib-devel-1.2.13-5.fc40.s390x                                                

Complete!
Finish: build setup for percolator-3.06.04-1.fc40.src.rpm
Start: rpmbuild percolator-3.06.04-1.fc40.src.rpm
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1701993600
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.w4GVdl
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf percolator-rel-3-06-04
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/percolator-rel-3-06-04.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd percolator-rel-3-06-04
+ rm -rf /builddir/build/BUILD/percolator-rel-3-06-04-SPECPARTS
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-rel-3-06-04-SPECPARTS
+ /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
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.r9u62h
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-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-3-06-04
+ export 'CXXFLAGS=-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ mkdir -p percolator
~/build/BUILD/percolator-rel-3-06-04/percolator ~/build/BUILD/percolator-rel-3-06-04
+ pushd percolator
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-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 -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=s390x ..
-- The C compiler identification is GNU 13.2.1
-- The CXX compiler identification is GNU 13.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- CMAKE_PREFIX_PATH = ../
-- XML_SUPPORT = ON
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = s390x
-- TOOL CHAIN FILE = 
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages:
-- Found Xerces-C: /usr/lib64/libxerces-c.so
--               : /usr/include
--        Version: 3.2.3
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- Locating CodeSynthesis library with XSDDIR set to 
-- Package CodeSynthesis XSD found: /usr/include, /usr/bin/xsdcxx
-- RPC found, will include headers from: /usr/include/tirpc
-- and libraries from                  : /usr/lib64/libtirpc.so
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.46.0") found components: filesystem system 
-- Found GTest: /usr/lib64/cmake/GTest/GTestConfig.cmake (found version "1.14.0")  
-- Using installed GoogleTest at: 
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.46.0")  
-- Configuring done (1.2s)
-- Generating done (0.0s)
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-3-06-04/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-3-06-04 -B/builddir/build/BUILD/percolator-rel-3-06-04/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color="
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color="
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[  2%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/Globals.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[  3%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/Logger.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[  4%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/MyException.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/Option.cpp
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/picked_protein/Database.cpp
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/picked_protein/Peptide.cpp
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/picked_protein/PeptideConstraint.cpp
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/picked_protein/PeptideSrc.cpp
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/percolator/src/percolator_in.cxx
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/picked_protein/PickedProteinCaller.cpp
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/picked_protein/Protein.cpp
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-3-06-04/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/picked_protein/Protein.cpp: In member function ‘PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/picked_protein/ProteinPeptideIterator.cpp
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/cmake -E cmake_link_script CMakeFiles/picked_protein.dir/link.txt --verbose=1
/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
/usr/bin/ranlib libpicked_protein.a
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dscal.c.o -MF CMakeFiles/blas.dir/dscal.c.o.d -o CMakeFiles/blas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/dscal.c
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/cmake -P CMakeFiles/blas.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/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
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a - CMakeFiles/blas.dir/dscal.c.o
/usr/bin/ranlib libblas.a
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake "--color="
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cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/percolator/src/percolator_out.cxx
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[ 24%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/fido/BasicBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/StringTable.h:9,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:6:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘void BasicBigraph::clonePSM(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:185:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  185 |   for (int k = 0; k < s.size(); k++) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:191:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  191 |   for (int k = 0; k < s.size(); k++) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:200:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  200 |   for (int k = 0; k < associatedProteinsBySection.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:211:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  211 |     for (int j = 0; j<associatedProteinsBySection[k].size(); j++)
      |                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:217:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  217 |   for (int k = 0; k < associatedProteinsBySection.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:218:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  218 |     for (int j = 0; j < associatedProteinsBySection[k].size(); j++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘BasicBigraph BasicBigraph::buildSubgraph(const Set&, const Set&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  265 |   for (int k = 0; k < result.PSMsToProteins.associations.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:274:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  274 |   for (int k = 0; k < result.proteinsToPSMs.associations.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘int BasicBigraph::markSectionPartitions()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  384 |   for (int k = 0; k < groups.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:9:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp: In instantiation of ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    9 |   for (int k = 0; k < rhs.size(); k++) {
      |                   ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array<T>::operator==(const Array<T>&) const [with T = int]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23:   required from ‘int HashTable<D>::searchList(const std::__cxx11::list<Node>&, const D&) const [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8:   required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16:   required from ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  267 |   for (int k=0; k<size(); k++) {
      |                 ~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 25%] Building CXX object src/CMakeFiles/perclibrary.dir/parser.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/parser.cxx
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx: In constructor ‘parser_impl::parser_impl()’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/parser.cxx:102:22: warning:   ‘xercesc_3_2::DOMImplementation& parser_impl::dom_impl_’ [-Wreorder]
  102 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
  144 | parser_impl::parser_impl() : clean_(true),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/parser.cxx:178:14: warning: unused variable ‘n’ [-Wunused-variable]
  178 |       size_t n(s.size());
      |              ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:170:9: warning: unused variable ‘i’ [-Wunused-variable]
  170 |     int i(1);
      |         ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 27%] Building CXX object src/CMakeFiles/perclibrary.dir/serializer.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/serializer.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 29%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/BaseSpline.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.cpp:24:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
[ 30%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/MassHandler.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 31%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/PSMDescription.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.cpp:21:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h: In constructor ‘PSMDescription::PSMDescription()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h:126:15: warning: ‘PSMDescription::peptide’ will be initialized after [-Wreorder]
  126 |   std::string peptide;
      |               ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h:122:7: warning:   ‘int PSMDescription::specFileNr’ [-Wreorder]
  122 |   int specFileNr;
      |       ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.cpp:23:1: warning:   when initialized here [-Wreorder]
   23 | PSMDescription::PSMDescription() :
      | ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h: In constructor ‘PSMDescription::PSMDescription(const std::string&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h:126:15: warning: ‘PSMDescription::peptide’ will be initialized after [-Wreorder]
  126 |   std::string peptide;
      |               ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h:122:7: warning:   ‘int PSMDescription::specFileNr’ [-Wreorder]
  122 |   int specFileNr;
      |       ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.cpp:28:1: warning:   when initialized here [-Wreorder]
   28 | PSMDescription::PSMDescription(const std::string& pep) :
      | ^~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 32%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/ResultHolder.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 26%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/fido/BasicGroupBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘void BasicGroupBigraph::groupProteinsBy(const Array<Set>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:47:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   47 |   for (int k = 0; k < groups.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:58:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   58 |   for (int k = 0; k < groups.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberAssociatedProteins(int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:79:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   79 |   for (int k=0; k<s.size(); k++) {
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberActiveAssociatedProteins(int, const Array<Counter>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:90:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   90 |   for (int k=0; k<s.size(); k++) {
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityE(const Model&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  100 |   for (int k=0; k<result.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::probabilityN(const Model&, const Array<Counter>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:168:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  168 |   for (int k=0; k<n.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::logNumberOfConfigurations() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:179:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  179 |   for (int k = 0; k < originalN.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::eCorrection(const Model&, const Array<Counter>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:252:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |   for (int k=0; k<result.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityRGivenN(const Array<Counter>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:289:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  289 |   for (int k=0; k<result.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityEOverAllAlphaBeta(const GridModel&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  322 |   for ( int k=0; k<result.size(); k++) {
      |                  ~^~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp: In instantiation of ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    9 |   for (int k = 0; k < rhs.size(); k++) {
      |                   ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array<T>::operator==(const Array<T>&) const [with T = int]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23:   required from ‘int HashTable<D>::searchList(const std::__cxx11::list<Node>&, const D&) const [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8:   required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16:   required from ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  267 |   for (int k=0; k<size(); k++) {
      |                 ~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 33%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/XMLInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h:30,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h: In constructor ‘XMLInterface::XMLInterface(const std::string&, const std::string&, bool, bool, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h:119:8: warning: ‘XMLInterface::reportPepXML_’ will be initialized after [-Wreorder]
  119 |   bool reportPepXML_;
      |        ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h:111:8: warning:   ‘bool XMLInterface::printDecoys_’ [-Wreorder]
  111 |   bool printDecoys_, printExpMass_;
      |        ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:58:1: warning:   when initialized here [-Wreorder]
   58 | XMLInterface::XMLInterface(const std::string& outputFN,
      | ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/XMLInterface.cpp:258:26: warning: unused variable ‘numFeatures’ [-Wunused-variable]
  258 |       const unsigned int numFeatures = FeatureNames::getNumFeatures();
      |                          ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp: In member function ‘void XMLInterface::writePepXML_PSMs(Scores&, double, std::string)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:641:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  641 |     if (sh->q < selectionFdr_)
      |     ^~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:643:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  643 |       index++;
      |       ^~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 34%] Building CXX object src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/fido/GroupPowerBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<double> GroupPowerBigraph::proteinProbs()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:10:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   10 |   for (int k = 0; k < subgraphs_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getGroupProtNames()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:22:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   22 |   for (int k = 0; k < subgraphs_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::printProteinWeights() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:34:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |   for (int k = 0; k < sorted.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsPercolator(std::vector<ProteinScoreHolder>&, std::map<std::__cxx11::basic_string<char>, long unsigned int>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:48:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   48 |   for (; k < sorted.size(); k++) {
      |          ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinNames(std::vector<std::vector<std::__cxx11::basic_string<char> > >&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:77:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   77 |   for (int k = 0; k < groupProtNames_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsAndNames(std::vector<std::vector<std::__cxx11::basic_string<char> > >&, std::vector<double>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:94:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   94 |   for (int k=0; k<sorted.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘double GroupPowerBigraph::getLogNumberStates() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:111:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  111 |   for (int k=0; k<subgraphs_.size(); k++) {
      |                 ~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<BasicBigraph> GroupPowerBigraph::iterativePartitionSubgraphs(BasicBigraph&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:128:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  128 |   for (int k = 0; k < preResult.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::initialize(BasicBigraph&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:188:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  188 |     for (int k = 0; k < subBasic.size(); k++) {
      |                     ~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<std::__cxx11::basic_string<char> > GroupPowerBigraph::peptideNames() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:202:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  202 |   for (int k = 0; k < subgraphs_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘std::pair<Array<Array<std::__cxx11::basic_string<char> > >, Array<double> > GroupPowerBigraph::getDescendingProteinsAndWeights() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:210:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  210 |   for (int k = 0; k < sorted.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:222:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  222 |   for (int k = 0; k < sorted.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 37%] Building CXX object src/fido/CMakeFiles/fido.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 38%] Building CXX object src/fido/CMakeFiles/fido.dir/Random.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/fido/Random.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp: In static member function ‘static void Random::fillRandomUniform(Array<double>&, double, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp:65:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   65 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 39%] Building CXX object src/fido/CMakeFiles/fido.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/fido/Set.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  142 |   for (int k=0; k<size()-1; k++) {
      |                 ~^~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp: In member function ‘int SetHandler::getOptionalFields(const std::string&, std::vector<OptionalField>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp:91:27: warning: variable ‘hasRt’ set but not used [-Wunused-but-set-variable]
   91 |   bool hasScannr = false, hasRt = false, hasDm = false;
      |                           ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp:91:42: warning: unused variable ‘hasDm’ [-Wunused-variable]
   91 |   bool hasScannr = false, hasRt = false, hasDm = false;
      |                                          ^~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 41%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/StdvNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 40%] Building CXX object src/fido/CMakeFiles/fido.dir/Vector.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/fido/Vector.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:382:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  382 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:392:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  392 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:530:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  530 |   for (int k=0; k<result.size(); k++)
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:542:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  542 |   for (int k=0; k<u.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:545:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  545 |       if ( k != u.size() - 1 )
      |            ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:559:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  559 |   for (int i=0; i<s.size(); i++)
      |                 ~^~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 44%] Linking CXX static library libfido.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 44%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 43%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/svm.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/svm.cpp: In function ‘svm_train’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/svm.cpp:42:38: warning: argument 1 range [18446744056529682432, 18446744073709551608] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   42 | #define Malloc(type,n) (type *)malloc((static_cast<std::size_t>(n))*sizeof(type))
      |                                ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/std_abs.h:38,
                 from /usr/include/c++/13/cmath:49,
                 from /usr/include/c++/13/math.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/svm.cpp:1:
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:28,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:29:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h: In constructor ‘CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, unsigned int, bool, unsigned int, bool, unsigned int, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:100:8: warning: ‘CrossValidation::trainBestPositive_’ will be initialized after [-Wreorder]
  100 |   bool trainBestPositive_;
      |        ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:89:16: warning:   ‘unsigned int CrossValidation::numThreads_’ [-Wreorder]
   89 |   unsigned int numThreads_;
      |                ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:32:1: warning:   when initialized here [-Wreorder]
   32 | CrossValidation::CrossValidation(bool quickValidation,
      | ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::preIterationSetup(Scores&, SanityCheck*, Normalizer*, FeatureMemoryPool&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:110:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  110 |     for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) {
      |                             ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(Normalizer*, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:296:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<candidateCposCfrac>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  296 |    for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++){
      |                          ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::mergeCpCnPairs(double, options&, std::vector<std::vector<Scores> >&, const std::vector<double>&, const std::vector<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:370:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  370 |   for (set = 0; set < numFolds_; ++set) {
      |                 ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:410:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  410 |     for (set = 0; set < numFolds_; ++set) {
      |                   ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:441:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  441 |   for (set = 0; set < numFolds_; ++set) {
      |                 ~~~~^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/Enzyme.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 45%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/Caller.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h: In constructor ‘Caller::Caller()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:111:27: warning: ‘Caller::analytics_’ will be initialized after [-Wreorder]
  111 |     skipNormalizeScores_, analytics_;
      |                           ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:97:8: warning:   ‘bool Caller::xmlPrintDecoys_’ [-Wreorder]
   97 |   bool xmlPrintDecoys_, xmlPrintExpMass_;
      |        ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp:36:1: warning:   when initialized here [-Wreorder]
   36 | Caller::Caller() :
      | ^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:110:48: warning: ‘Caller::trainBestPositive_’ will be initialized after [-Wreorder]
  110 |   bool reportEachIteration_, quickValidation_, trainBestPositive_,
      |                                                ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:108:59: warning:   ‘unsigned int Caller::numThreads_’ [-Wreorder]
  108 |   unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_;
      |                                                           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp:36:1: warning:   when initialized here [-Wreorder]
   36 | Caller::Caller() :
      | ^~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/Globals.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp: In member function ‘virtual void NoNormalizer::unnormalizeweight(const std::vector<double>&, std::vector<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp:40:10: warning: unused variable ‘sum’ [-Wunused-variable]
   40 |   double sum = 0;
      |          ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp: In member function ‘virtual void NoNormalizer::normalizeweight(const std::vector<double>&, std::vector<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp:49:10: warning: unused variable ‘sum’ [-Wunused-variable]
   49 |   double sum = 0;
      |          ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/Normalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/UniNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/SanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.h:87:8: warning: ‘SanityCheck::concatenatedSearch_’ will be initialized after [-Wreorder]
   87 |   bool concatenatedSearch_;
      |        ^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.h:72:10: warning:   ‘double SanityCheck::test_fdr_’ [-Wreorder]
   72 |   double test_fdr_, initial_train_fdr_;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp:31:1: warning:   when initialized here [-Wreorder]
   31 | SanityCheck::SanityCheck() :
      | ^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/FeatureNames.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/LogisticRegression.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.cpp:27:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 54%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/DataSet.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 58%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/ProteinProbEstimator.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:238:16: warning: ‘ProteinProbEstimator::absenceRatio_’ will be initialized after [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |                ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:238:10: warning:   ‘double ProteinProbEstimator::pi0_’ [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:242:16: warning: ‘ProteinProbEstimator::numberTargetProteins_’ will be initialized after [-Wreorder]
  242 |   unsigned int numberTargetProteins_;
      |                ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:237:8: warning:   ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder]
  237 |   bool usePi0_;
      |        ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:243:15: warning: ‘ProteinProbEstimator::decoyPattern_’ will be initialized after [-Wreorder]
  243 |   std::string decoyPattern_;
      |               ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:240:10: warning:   ‘double ProteinProbEstimator::fdr_’ [-Wreorder]
  240 |   double fdr_;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/PosteriorEstimator.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.cpp:37:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/ProteinFDRestimator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/PseudoRandom.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/SqtSanityCheck.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
[ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/ssl.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/PackedVector.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.cpp:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/PackedMatrix.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedMatrix.h:11,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedMatrix.cpp:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/Matrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/Matrix.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp: In member function ‘const Matrix& Matrix::operator=(const Array<Array<double> >&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp:10:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   10 |   for (int k=0; k<rhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp: In function ‘Array<Array<double> > operator-(const Array<Array<double> >&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp:519:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  519 |   for (int k=0; k<result.size(); k++)
      |                 ~^~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 70%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/Logger.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/MyException.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/FidoInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/FidoInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.h:20,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/FidoInterface.h:110:10: warning: ‘FidoInterface::mseThreshold_’ will be initialized after [-Wreorder]
  110 |   double mseThreshold_;
      |          ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.h:106:8: warning:   ‘bool FidoInterface::doGridSearch_’ [-Wreorder]
  106 |   bool doGridSearch_;
      |        ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.cpp:76:1: warning:   when initialized here [-Wreorder]
   76 | FidoInterface::FidoInterface(double alpha, double beta, double gamma,
      | ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.cpp: In member function ‘double FidoInterface::estimatePriors(Scores&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.cpp:132:10: warning: variable ‘prior’ set but not used [-Wunused-but-set-variable]
  132 |   double prior, prior2, prior3, prior4;
      |          ^~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 74%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/ProteinScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.h: In constructor ‘ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.h:108:8: warning: ‘ProteinScoreHolder::isDecoy_’ will be initialized after [-Wreorder]
  108 |   bool isDecoy_;
      |        ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.h:106:7: warning:   ‘int ProteinScoreHolder::groupId_’ [-Wreorder]
  106 |   int groupId_;
      |       ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 62%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/Scores.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp:35:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp: In member function ‘void ScoreHolder::printPepXML(std::ostream&, std::map<char, float>&, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp:163:16: warning: unused variable ‘native_id’ [-Wunused-variable]
  163 |   unsigned int native_id = scan - 1;
      |                ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp:167:10: warning: unused variable ‘RT’ [-Wunused-variable]
  167 |   double RT = pPSM->getRetentionTime();
      |          ^~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/FeatureMemoryPool.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/PickedProteinInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:27,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h: In constructor ‘PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:86:10: warning: ‘PickedProteinInterface::maxPeptidePval_’ will be initialized after [-Wreorder]
   86 |   double maxPeptidePval_;
      |          ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:85:8: warning:   ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |        ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:85:33: warning: ‘PickedProteinInterface::reportDuplicateProteins_’ will be initialized after [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:83:26: warning:   ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder]
   83 |   ProteinInferenceMethod protInferenceMethod_;
      |                          ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 79%] Building CXX object src/CMakeFiles/perclibrary.dir/Timer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Timer.cpp.o -MF CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Timer.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o -MF CMakeFiles/perclibrary.dir/TmpDir.cpp.o.d -o CMakeFiles/perclibrary.dir/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -MF CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o.d -o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/ValidateTabFile.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ValidateTabFile.h:6,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ValidateTabFile.cpp:1:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o -MF CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o.d -o CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/GoogleAnalytics.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 82%] Linking CXX static library libperclibrary.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/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/MassHandler.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.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/NoNormalizer.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/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 CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o CMakeFiles/perclibrary.dir/Timer.cpp.o CMakeFiles/perclibrary.dir/TmpDir.cpp.o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
/usr/bin/ranlib libperclibrary.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 84%] Built target perclibrary
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend
/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-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
[ 87%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/qvality/qvality_main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/./PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/./BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/./LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/./PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/qvality/qvality_main.cpp:20:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
[ 86%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/main.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/main.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 88%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-rel-3-06-04/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 -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc -rdynamic CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality   -L/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src  ../libperclibrary.a ../fido/libfido.a 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 90%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -MF CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o.d -o CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/Unit_tests_Percolator_main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
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[ 91%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Fido.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Fido.cpp:24:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 93%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Option.cpp
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[ 94%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp:23:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 95%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:20:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp: In member function ‘int SetHandlerTest::testInput(SetHandler*, const char*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:65:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
   65 |     if (n > 0)
      |        ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 96%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp:23:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 97%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp:24:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 98%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++14 -MD -MT tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -MF CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o.d -o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:19:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp: In member function ‘virtual void CrossValidationTest_doStepTest_Test::TestBody()’:
/builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:140:9: warning: unused variable ‘numInit’ [-Wunused-variable]
  140 |     int numInit = crossValidation->preIterationSetup(scores, pCheck, pNorm,
      |         ^~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 89%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-rel-3-06-04/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 -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc -rdynamic CMakeFiles/percolator.dir/main.cpp.o -o percolator  libperclibrary.a blas/libblas.a fido/libfido.a picked_protein/libpicked_protein.a -lxerces-c -ltirpc -lstdc++ /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_system.a /usr/lib64/libboost_atomic.a 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In function ‘readRawSequence’,
    inlined from ‘parseProteinFastaFile’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/picked_protein/Protein.cpp: In member function ‘parseProteinFastaFile’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
[100%] Built target percolator
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[100%] Linking CXX executable gtest_unit
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_unit.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc -rdynamic CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o gtest_unit  ../../../src/libperclibrary.a ../../../src/blas/libblas.a ../../../src/fido/libfido.a -lpthread /usr/lib64/libgtest_main.so.1.14.0 /usr/lib64/libgtest.so.1.14.0 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[100%] Built target gtest_unit
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ mkdir -p fido
+ pushd fido
~/build/BUILD/percolator-rel-3-06-04/fido ~/build/BUILD/percolator-rel-3-06-04
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-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 -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc' -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTARGET_ARCH=s390x ../src/fido
-- The C compiler identification is GNU 13.2.1
-- The CXX compiler identification is GNU 13.2.1
-- 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 (0.5s)
-- Generating done (0.0s)
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-3-06-04/fido
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -B/builddir/build/BUILD/percolator-rel-3-06-04/fido --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/fido/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/fido'
cd /builddir/build/BUILD/percolator-rel-3-06-04/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/fido /builddir/build/BUILD/percolator-rel-3-06-04/fido /builddir/build/BUILD/percolator-rel-3-06-04/fido/CMakeFiles/fido.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
/usr/bin/make  -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/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 -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/BasicGroupBigraph.o -MF CMakeFiles/fido.dir/BasicGroupBigraph.o.d -o CMakeFiles/fido.dir/BasicGroupBigraph.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
../src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   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:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
../src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:84:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
   84 | 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-3-06-04/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:107:37: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  107 | 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:117:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  117 | 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:129:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  129 | 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:138:38: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  138 | 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:144:43: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  144 | 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:150:33: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  150 | 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
      |            ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘void BasicGroupBigraph::groupProteinsBy(const Array<Set>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:47:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   47 |   for (int k = 0; k < groups.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:58:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   58 |   for (int k = 0; k < groups.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberAssociatedProteins(int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:79:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   79 |   for (int k=0; k<s.size(); k++) {
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberActiveAssociatedProteins(int, const Array<Counter>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:90:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   90 |   for (int k=0; k<s.size(); k++) {
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityE(const Model&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  100 |   for (int k=0; k<result.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::probabilityN(const Model&, const Array<Counter>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:168:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  168 |   for (int k=0; k<n.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::logNumberOfConfigurations() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:179:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  179 |   for (int k = 0; k < originalN.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::eCorrection(const Model&, const Array<Counter>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:252:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |   for (int k=0; k<result.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityRGivenN(const Array<Counter>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:289:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  289 |   for (int k=0; k<result.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityEOverAllAlphaBeta(const GridModel&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  322 |   for ( int k=0; k<result.size(); k++) {
      |                  ~^~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp: In instantiation of ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    9 |   for (int k = 0; k < rhs.size(); k++) {
      |                   ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array<T>::operator==(const Array<T>&) const [with T = int]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23:   required from ‘int HashTable<D>::searchList(const std::__cxx11::list<Node>&, const D&) const [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8:   required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16:   required from ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  267 |   for (int k=0; k<size(); k++) {
      |                 ~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 12%] Building CXX object CMakeFiles/fido.dir/BasicBigraph.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/BasicBigraph.o -MF CMakeFiles/fido.dir/BasicBigraph.o.d -o CMakeFiles/fido.dir/BasicBigraph.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:4:
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
../src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   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:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
../src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:84:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
   84 | 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-3-06-04/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:107:37: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  107 | 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:117:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  117 | 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:129:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  129 | 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:138:38: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  138 | 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:144:43: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  144 | 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:150:33: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  150 | 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-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/StringTable.h:9,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:6:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘void BasicBigraph::clonePSM(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:185:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  185 |   for (int k = 0; k < s.size(); k++) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:191:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  191 |   for (int k = 0; k < s.size(); k++) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:200:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  200 |   for (int k = 0; k < associatedProteinsBySection.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:211:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  211 |     for (int j = 0; j<associatedProteinsBySection[k].size(); j++)
      |                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:217:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  217 |   for (int k = 0; k < associatedProteinsBySection.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:218:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  218 |     for (int j = 0; j < associatedProteinsBySection[k].size(); j++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘BasicBigraph BasicBigraph::buildSubgraph(const Set&, const Set&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  265 |   for (int k = 0; k < result.PSMsToProteins.associations.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:274:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  274 |   for (int k = 0; k < result.proteinsToPSMs.associations.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘int BasicBigraph::markSectionPartitions()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  384 |   for (int k = 0; k < groups.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:9:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp: In instantiation of ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    9 |   for (int k = 0; k < rhs.size(); k++) {
      |                   ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array<T>::operator==(const Array<T>&) const [with T = int]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23:   required from ‘int HashTable<D>::searchList(const std::__cxx11::list<Node>&, const D&) const [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8:   required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16:   required from ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  267 |   for (int k=0; k<size(); k++) {
      |                 ~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/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 -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Numerical.o -MF CMakeFiles/fido.dir/Numerical.o.d -o CMakeFiles/fido.dir/Numerical.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/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 -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Random.o -MF CMakeFiles/fido.dir/Random.o.d -o CMakeFiles/fido.dir/Random.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp: In static member function ‘static void Random::fillRandomUniform(Array<double>&, double, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp:65:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   65 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/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 -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Set.o -MF CMakeFiles/fido.dir/Set.o.d -o CMakeFiles/fido.dir/Set.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  142 |   for (int k=0; k<size()-1; k++) {
      |                 ~^~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/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 -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/Vector.o -MF CMakeFiles/fido.dir/Vector.o.d -o CMakeFiles/fido.dir/Vector.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:382:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  382 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:392:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  392 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:530:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  530 |   for (int k=0; k<result.size(); k++)
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:542:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  542 |   for (int k=0; k<u.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:545:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  545 |       if ( k != u.size() - 1 )
      |            ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:559:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  559 |   for (int i=0; i<s.size(); i++)
      |                 ~^~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/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 -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -MD -MT CMakeFiles/fido.dir/GroupPowerBigraph.o -MF CMakeFiles/fido.dir/GroupPowerBigraph.o.d -o CMakeFiles/fido.dir/GroupPowerBigraph.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
../src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   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:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
../src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:84:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
   84 | 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-3-06-04/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:107:37: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  107 | 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:117:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  117 | 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:129:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  129 | 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:138:38: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  138 | 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:144:43: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  144 | 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:150:33: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  150 | 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
      |            ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<double> GroupPowerBigraph::proteinProbs()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:10:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   10 |   for (int k = 0; k < subgraphs_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getGroupProtNames()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:22:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘lonmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
g unsigned int’} [-Wsign-compare]
   22 |   for (int k = 0; k < subgraphs_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::printProteinWeights() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:34:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |   for (int k = 0; k < sorted.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsPercolator(std::vector<ProteinScoreHolder>&, std::map<std::__cxx11::basic_string<char>, long unsigned int>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:48:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   48 |   for (; k < sorted.size(); k++) {
      |          ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinNames(std::vector<std::vector<std::__cxx11::basic_string<char> > >&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:77:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   77 |   for (int k = 0; k < groupProtNames_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsAndNames(std::vector<std::vector<std::__cxx11::basic_string<char> > >&, std::vector<double>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:94:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   94 |   for (int k=0; k<sorted.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘double GroupPowerBigraph::getLogNumberStates() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:111:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  111 |   for (int k=0; k<subgraphs_.size(); k++) {
      |                 ~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<BasicBigraph> GroupPowerBigraph::iterativePartitionSubgraphs(BasicBigraph&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:128:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  128 |   for (int k = 0; k < preResult.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::initialize(BasicBigraph&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:188:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  188 |     for (int k = 0; k < subBasic.size(); k++) {
      |                     ~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<std::__cxx11::basic_string<char> > GroupPowerBigraph::peptideNames() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:202:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  202 |   for (int k = 0; k < subgraphs_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘std::pair<Array<Array<std::__cxx11::basic_string<char> > >, Array<double> > GroupPowerBigraph::getDescendingProteinsAndWeights() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:210:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  210 |   for (int k = 0; k < sorted.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:222:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  222 |   for (int k = 0; k < sorted.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/fido'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[100%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/fido/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ mkdir -p converters
+ pushd converters
~/build/BUILD/percolator-rel-3-06-04/converters ~/build/BUILD/percolator-rel-3-06-04
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-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 -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc' -DCMAKE_BUILD_TYPE:STRING=Release -DPERCOLATOR-CONVERTERS_BINARY_DIR:STATIC=converters -DCMAKE_SKIP_INSTALL_RPATH:BOOL=YES -DCMAKE_SKIP_RPATH:BOOL=YES -DTokyoCabinet_INCLUDE_DIR=/usr/include -DTokyoCabinet_LIBRARY=/usr/lib64/libtokyocabinet.so -DSERIALIZE=TokyoCabinet -DTARGET_ARCH=s390x ../src/converters
-- The C compiler identification is GNU 13.2.1
-- The CXX compiler identification is GNU 13.2.1
-- 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-3-06-04/src/converters/../..
-- CMAKE_PREFIX_PATH = ../
-- TARGET_ARCH = s390x
-- TOOL CHAIN FILE = 
-- SERIALIZE = TokyoCabinet
-- PROFILING = 
-- Using Tokyo Cabinet Serialization scheme
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages..
-- Found Xerces-C: /usr/lib64/libxerces-c.so
--               : /usr/include
--        Version: 3.2.3
-- Package CodeSynthesis XSD found: /usr/include
--                      Executable: /usr/bin/xsdcxx
-- 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-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", 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  
-- RPC found, will include headers from: /usr/include/tirpc
-- and libraries from                  : /usr/lib64/libtirpc.so
-- Generating classes from xsd-schema using CodeSynthesis
-- Generating /builddir/build/BUILD/percolator-rel-3-06-04/converters/gaml_tandem1.0.cxx;/builddir/build/BUILD/percolator-rel-3-06-04/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 (1.2s)
-- Generating done (0.0s)
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-3-06-04/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-3-06-04/src/converters -B/builddir/build/BUILD/percolator-rel-3-06-04/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake "--color="
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake "--color="
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make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
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make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake "--color="
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[  7%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/RAMP/ramp_base64.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[  8%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function ‘RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/RAMP/ramp.h:134,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:34:
In function ‘*strchr’,
    inlined from ‘readPeaks(RAMPFILE*, long)’ at /builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/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-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function ‘rampSelfTest(char*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:2054:12: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
 2054 |     strncpy(buf, filename, sizeof(buf));
      |            ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 10%] Linking CXX static library libRAMP.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/cmake -P CMakeFiles/RAMP.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/cmake -E cmake_link_script CMakeFiles/RAMP.dir/link.txt --verbose=1
/usr/bin/ar qc libRAMP.a CMakeFiles/RAMP.dir/ramp_base64.cpp.o CMakeFiles/RAMP.dir/ramp.cpp.o
/usr/bin/ranlib libRAMP.a
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/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx: In constructor ‘parser_impl::parser_impl()’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/parser.cxx:102:22: warning:   ‘xercesc_3_2::DOMImplementation& parser_impl::dom_impl_’ [-Wreorder]
  102 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
  144 | parser_impl::parser_impl() : clean_(true),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/parser.cxx:178:14: warning: unused variable ‘n’ [-Wunused-variable]
  178 |       size_t n(s.size());
      |              ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:170:9: warning: unused variable ‘i’ [-Wunused-variable]
  170 |     int i(1);
      |         ^
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In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.H:28,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:16:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In function ‘LazyMatrix* flip_lazy_matrix(LazyMatrix&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/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-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In constructor ‘LazyMatrix::LazyMatrix(int, int, sparse_level, FILE*, off_t)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:39:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   39 |     for ( std::size_t i = 0 ; i < nrows ; i++ ) {
      |                               ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:44:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   44 |     for ( std::size_t i = 0 ; i < nrows; i++ ) {
      |                               ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In copy constructor ‘LazyMatrix::LazyMatrix(const self&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:56:6: warning: value computed is not used [-Wunused-value]
   56 |      *data_copies++;
      |      ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::copy_m_flip(const self&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::set_col(std::vector<float>&, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:150:39: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  150 |           for ( std::size_t i = 0 ; i < nrows ; i++ ) {
      |                                     ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::_get_row_retain(std::vector<float>&, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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[static_cast<std::size_t>(i)]->begin();
      |                                           ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_cols(int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:290:72: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  290 |           for ( std::size_t i = static_cast<std::size_t>(start_idx); i < stop_idx ; i++ ) {
      |                                                                      ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_start_cols(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:298:39: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  298 |           for ( std::size_t i = 0 ; i < rows() ; i++ ) {
      |                                     ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_stop_cols(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:305:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  305 |           for ( std::size_t i =0 ; i < rows() ; i++ ) {
      |                                    ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::column_shift(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/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-3-06-04/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-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::linear_shift(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:393:62: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  393 |     for ( std::size_t i = static_cast<std::size_t>(shift); i < nrows; i++ ) {
      |                                                            ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:409:31: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
igned int’} and ‘int’ [-Wsign-compare]
  409 |     for ( uint i = offset ; i < nrows - static_cast<int>(offset); i++ ) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:412:76: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  412 |     for ( uint i = static_cast<uint>(nrows - static_cast<int>(offset)) ; i < nrows; i++ ) {
      |                                                                          ~~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 42%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/MSConvertFile.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 44%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/MSObject.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 46%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/MSReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::writeFile(const char*, bool, MSObject&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:509:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  509 |   for(unsigned int j=0;j<m.size();j++){
      |                        ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::writeSqlite(const char*, MSObject&, char*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/Spectrum.h:4,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.h:4,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSToolkitTypes.h:54:14: note: ‘MSHeader::header’ declared here
   54 |         char header[16][128];
      |              ^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::appendFile(Spectrum&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/MSReader.cpp:756:17: warning: variable ‘sizeM’ set but not used [-Wunused-but-set-variable]
  756 |   unsigned long sizeM;
      |                 ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:757:17: warning: variable ‘sizeI’ set but not used [-Wunused-but-set-variable]
  757 |   unsigned long sizeI;
      |                 ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::appendFile(char*, MSObject&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1016:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1016 |       for(i=0;i<m.size();i++) writeTextSpec(fileOut,m.at(i));
      |               ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1025:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1025 |       for(i=0;i<m.size();i++){
      |               ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1034:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1034 |       for(i=0;i<m.size();i++){
      |               ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1043:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1043 |       for(i=0;i<m.size();i++){
      |               ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘bool MSReader::executeSqlStmt(Spectrum&, char*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1187:7: warning: unused variable ‘charge’ [-Wunused-variable]
 1187 |   int charge=-1;
      |       ^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::writeCompressSpec(FILE*, Spectrum&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/MSReader.cpp:1616:23: warning: variable ‘sizeM’ set but not used [-Wunused-but-set-variable]
 1616 |         unsigned long sizeM;
      |                       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1617:23: warning: variable ‘sizeI’ set but not used [-Wunused-but-set-variable]
 1617 |         unsigned long sizeI;
      |                       ^~~~~
In file included from /usr/include/stdio.h:980,
                 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:2227,
                 from /usr/include/c++/13/vector:62,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.h:5:
In function ‘sprintf’,
    inlined from ‘MSReader::appendFile(Spectrum&)’ at /builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘MSReader::appendFile(Spectrum&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:853:7: note: ‘lastScanID’ was declared here
  853 |   int lastScanID;
      |       ^~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 48%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/MSSingleScan.cpp
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[ 50%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/MSTAllRT.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSTAllRT.cpp: In function ‘int main(int, char**)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSTAllRT.cpp:26:22: warning: variable ‘ff’ set but not used [-Wunused-but-set-variable]
   26 |         MSFileFormat ff;
      |                      ^~
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cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/MSTDemo.cpp
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[ 53%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/MSWarper.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSWarper.cpp:16:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSWarper.cpp:17:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable]
  594 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable]
  697 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  806 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  807 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function]
  808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:809:16: warning: ‘msmat* test_msmat(int, char**)’ declared ‘static’ but never defined [-Wunused-function]
  809 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:812:13: warning: ‘void output_bp_chrom(msmat&, char*)’ declared ‘static’ but never defined [-Wunused-function]
  812 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:813:17: warning: ‘msmat* msmat_from_fh(FILE*, sparse_level)’ declared ‘static’ but never defined [-Wunused-function]
  813 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:814:16: 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]
  814 | 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-3-06-04/src/converters/MSToolkit/msmat.H:48:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
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[ 55%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/Spectrum.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.cpp: In member function ‘bool Spectrum::getRawFilter(char*, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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)) {
      |      ~~^~~~~~~~~~~~~~~~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/converters/tandem2011.12.01.1.cxx
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[ 58%] 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/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/Reader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/SqtReader.cpp
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cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/crawutils.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:21:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘void crawutils::rankties(std::vector<float>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:261:9: warning: unused variable ‘start_idx’ [-Wunused-variable]
  261 |     int start_idx = -1;
      |         ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:262:9: warning: unused variable ‘stop_idx’ [-Wunused-variable]
  262 |     int stop_idx = -1;
      |         ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/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[static_cast<std::size_t>(i)].first == last_val) ) {
      |              ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:346:9: warning: unused variable ‘last_rank’ [-Wunused-variable]
  346 |     int last_rank = -1;
      |         ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘float crawutils::spectra_spearman_rank_corr_3(const std::vector<float>&, const std::vector<float>&, double, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:455:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  455 |     for ( std::size_t i = 0 ; i < (int)s1.size();  i++ ) {
      |                               ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘float crawutils::spectra_spearman_rank_corr_4(const std::vector<float>&, const std::vector<float>&, double, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:488:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  488 |     for ( std::size_t i = 0 ; i < (int)s1.size();  i++ ) {
      |                               ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/crawutils.cpp:976:23: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  976 |     for (idx = 1; idx < (int)y.size(); idx++)
      |                   ~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/crawutils.cpp:1090:10: warning: unused variable ‘last_tryp’ [-Wunused-variable]
 1090 |     bool last_tryp = false;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘float crawstats::pi0_from_StoreySplineFit(const std::vector<std::pair<float, float> >&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:1402:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1402 |   for (std::size_t i = 1; i <= n - 1; i++)
      |                           ~~^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 62%] 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/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MzidentmlReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MzidentmlReader.cpp: In member function ‘virtual void MzidentmlReader::getMaxMinCharge(const std::string&, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/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-3-06-04/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-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 66%] 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/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/SequestReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/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-3-06-04/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-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 64%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/msmat.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:17:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable]
  594 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable]
  697 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In constructor ‘transition_manager::transition_manager(std::vector<transition_info>)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:47:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<transition_info>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   47 |       for ( int  i = 0 ; i < transitions.size() ; i++ ) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::init_transitions_from_labels()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:76:24: 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]
   76 |    for ( int i = 0 ; i < labels.size() ; i++ ) {
      |                      ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::tabular_input(std::ifstream&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:107:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  107 |      for ( int mz_idx = 0 ; mz_idx < this->get_num_mzs() ; mz_idx++ ) {
      |                             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::zero_chrom(int, int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:185:70: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  185 |   for ( std::size_t i = static_cast<std::size_t>(start_scan_idx) ; i <= stop_scan_idx ; i++ ) {
      |                                                                    ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::retain_dist_set(int, std::vector<int>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:216:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  216 |     for ( int i = 0 ; i < this->get_num_rts() ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/msmat.cpp:225:9: warning: unused variable ‘set_idx’ [-Wunused-variable]
  225 |     int set_idx = 0;
      |         ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::retain_chrom(int, int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:251:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  251 |   for ( std::size_t i = 0 ; i < start_scan_idx ; i++ ) {
      |                             ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘int msmat::check_size_from_position() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:271:30: warning: comparison of integer expressions of different signedness: ‘off64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  271 |   if ( ( end_pos - cur_pos ) == get_num_mzs() * get_num_rts() * sizeof(float) ) {
      |        ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::calc_bp_chrom()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:668:36: warning: variable ‘scan_length’ set but not used [-Wunused-but-set-variable]
  668 |   std::size_t scan_idx, num_scans, scan_length;
      |                                    ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::pad_start_stop(int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:775:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  775 |                                   for ( int i = stop_mapped_coord+1 ; i < get_num_rts()  ; i++  ) {
      |                                                                       ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::time_interpolate(double, msmat&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1056:14: warning: variable ‘dim’ set but not used [-Wunused-but-set-variable]
 1056 |   matrix_dim dim = get_data_dim();
      |              ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::get_median() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1266:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1266 |   for ( int i = 0 ; i < this->get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1267:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1267 |     for ( int j = 0 ; j < this->get_num_cols() ; j++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::get_avg(int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/srmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
c/converters/MSToolkit/msmat.cpp:1282:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1282 |     if ( i < 0 || i >= get_num_rts()  ) {
      |                   ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::calc_twomat_num(const msmat&, double, double, int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1313:72: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1313 |                                      for ( int self_idx = 0 ; self_idx < get_num_rts() ; self_idx++ ) {
      |                                                               ~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1315:72: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1315 |                                        if ( other_idx < 0 || other_idx >= other.get_num_rts() ) {
      |                                                              ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::calc_mat_denom(double, int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1338:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1338 |     if ( i < 0 || i >= get_num_rts() ) {
      |                   ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::correlation_w_shift(const msmat&, int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1356:17: warning: unused variable ‘self’ [-Wunused-variable]
 1356 |   const msmat & self = *this;
      |                 ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘msmat_chroms* msmat_chroms::extract_mzidx_range(int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1411:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1411 |     for ( std::size_t i = 0;  i < r_stop - r_start ; i++ ) {
      |                               ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1410:9: warning: unused variable ‘foo’ [-Wunused-variable]
 1410 |     int foo = 5;
      |         ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘virtual void msmat_scans::get_chrom(int, std::vector<float>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1486:11: warning: unused variable ‘volatile_this’ [-Wunused-variable]
 1486 |   msmat * volatile_this;
      |           ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In function ‘msmat* test_msmat(int, char**)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1593:19: warning: variable ‘ti_file’ set but not used [-Wunused-but-set-variable]
 1593 |   FILE * o_file, *ti_file, *sg_file;
      |                   ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1593:29: warning: variable ‘sg_file’ set but not used [-Wunused-but-set-variable]
 1593 |   FILE * o_file, *ti_file, *sg_file;
      |                             ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_mzs_by_avg(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1816:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1816 |     new_cnt < mzs.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1818:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1818 |       for ( std::size_t i = 0 ; i < decimate_size ; i++ ) {
      |                                 ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_rts_by_avg(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1846:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1846 |     new_cnt < rts.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1848:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1848 |       for ( std::size_t i = 0 ; i < decimate_size ; i++ ) {
      |                                 ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_mzs_by_sample(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1868:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1868 |     new_cnt < mzs.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_rts_by_sample(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1886:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1886 |     new_cnt < rts.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘bool msmat::equals_data(const msmat&, double) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1909:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1909 |   for ( int i = 0 ; i < get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::sum_abs_diffs(const msmat&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1932:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1932 |   for ( int i = 0 ; i < get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1929:10: warning: unused variable ‘nrows’ [-Wunused-variable]
 1929 |   size_t nrows = get_num_rows();
      |          ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/msmat.cpp:1978:13: warning: unused variable ‘num_mzs’ [-Wunused-variable]
 1978 |   const int num_mzs = static_cast<int>(get_num_mzs());
      |             ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/msmat.cpp:2097:7: warning: unused variable ‘start_rt_idx’ [-Wunused-variable]
 2097 |   int start_rt_idx = this->rt_to_rtidx(start_rt);
      |       ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:2098:7: warning: unused variable ‘stop_rt_idx’ [-Wunused-variable]
 2098 |   int stop_rt_idx = this->rt_to_rtidx(stop_rt);
      |       ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  806 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  807 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function]
  808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1728:9: 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]
 1728 | msmat * msmat_from_thevoid
      |         ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1701:6: warning: ‘void output_bp_chrom(msmat&, char*)’ defined but not used [-Wunused-function]
 1701 | void output_bp_chrom( msmat & m, char * fname  ) {
      |      ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1570:9: warning: ‘msmat* test_msmat(int, char**)’ defined but not used [-Wunused-function]
 1570 | msmat * test_msmat ( int argc , char ** argv ) {
      |         ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/converters'
[ 69%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/msmat_base.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.cpp:16:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 71%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.H:20,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:19:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:20:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable]
  594 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable]
  697 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/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-3-06-04/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-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:361:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  361 |   for ( std::size_t i = c1_loc+1 ; i < key_last+1 ; i++ ) {
      |                                    ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:14: warning: unused variable ‘key_fields_len’ [-Wunused-variable]
  343 |   int c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |              ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:30: warning: unused variable ‘key_last_loc’ [-Wunused-variable]
  343 |   int c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |                              ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:44: warning: unused variable ‘key_data_len’ [-Wunused-variable]
  343 |   int c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |                                            ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/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-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:359:7: warning: unused variable ‘key_data_idx’ [-Wunused-variable]
  359 |   int key_data_idx;
      |       ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  806 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  807 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function]
  808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:809:16: warning: ‘msmat* test_msmat(int, char**)’ declared ‘static’ but never defined [-Wunused-function]
  809 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:812:13: warning: ‘void output_bp_chrom(msmat&, char*)’ declared ‘static’ but never defined [-Wunused-function]
  812 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:813:17: warning: ‘msmat* msmat_from_fh(FILE*, sparse_level)’ declared ‘static’ but never defined [-Wunused-function]
  813 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:814:16: 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]
  814 | 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-3-06-04/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-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:314:10: warning: ‘operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  314 |   delete k;
      |          ^
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:315:10: warning: ‘operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  315 |   delete v;
      |          ^
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/convertmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
ers/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::allocator<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-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:386:10: warning: ‘operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  386 |   delete values;
      |          ^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:381:37: note: returned from ‘operator new[](unsigned long)’
  381 |   float * values = new float[val_len];
      |                                     ^
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 73%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MSToolkit/msmat_test.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp:4:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable]
  594 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable]
  697 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp: In function ‘int main(int, char**)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp:13:12: warning: unused variable ‘m’ [-Wunused-variable]
   13 |   msmat  * m;
      |            ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  806 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  807 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function]
  808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:809:16: warning: ‘msmat* test_msmat(int, char**)’ declared ‘static’ but never defined [-Wunused-function]
  809 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:812:13: warning: ‘void output_bp_chrom(msmat&, char*)’ declared ‘static’ but never defined [-Wunused-function]
  812 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:813:17: warning: ‘msmat* msmat_from_fh(FILE*, sparse_level)’ declared ‘static’ but never defined [-Wunused-function]
  813 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:814:16: 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]
  814 | 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-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
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[ 75%] Linking CXX static library libMSToolkit.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/cmake -P CMakeFiles/MSToolkit.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/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
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[ 67%] 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/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/MsgfplusReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/MsgfplusReader.cpp:332:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
  332 |                           else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
      |                           ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:332:104: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
  332 |                           else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
      |                                                                                                        ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:271:14: warning: unused variable ‘peptide_length’ [-Wunused-variable]
  271 |     unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
      |              ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:290:12: warning: variable ‘SpecEValue’ set but not used [-Wunused-but-set-variable]
  290 |     double SpecEValue = 0.0;
      |            ^~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/FragSpectrumScanDatabase.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabase.cpp: In member function ‘std::string FragSpectrumScanDatabase::decoratePeptide(const percolatorInNs::peptideType&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabase.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   81 |     if (it->first <= peptideSeq.length()) {
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/TandemReader.cpp.o -MF CMakeFiles/converters.dir/TandemReader.cpp.o.d -o CMakeFiles/converters.dir/TandemReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp: In member function ‘virtual void TandemReader::getMaxMinCharge(const std::string&, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp:248:24: warning: catching polymorphic type ‘class MyException’ by value [-Wcatch-value=]
  248 |   } catch (MyException e) {
      |                        ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp:251:27: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
  251 |   } catch (std::exception e) {
      |                           ^
/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/src/converters/TandemReader.cpp:468:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  468 |     f_seq.push_back( charge == c ? 1.0 : 0.0);
      |                      ~~~~~~~^~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp: In member function ‘virtual void FragSpectrumScanDatabaseTokyoDB::putFSS(percolatorInNs::fragSpectrumScan&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp:165:10: warning: unused variable ‘valueSize’ [-Wunused-variable]
  165 |   size_t valueSize(buf.size ());
      |          ^~~~~~~~~
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/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/Interface.cpp.o -MF CMakeFiles/converters.dir/Interface.cpp.o.d -o CMakeFiles/converters.dir/Interface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.h: In constructor ‘Interface::Interface()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.h:50:14: warning: ‘Interface::xmlOutput’ will be initialized after [-Wreorder]
   50 |         bool xmlOutput;
      |              ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.h:47:21: warning:   ‘std::string Interface::outputFN’ [-Wreorder]
   47 |         std::string outputFN;
      |                     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.cpp:21:1: warning:   when initialized here [-Wreorder]
   21 | Interface::Interface() : xmlOutput(false), outputFN("") { }
      | ^~~~~~~~~
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/usr/bin/ranlib libconverters.a
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cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake "--color="
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake "--color="
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 92%] Building CXX object CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -MF CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o.d -o CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Sqt2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 91%] Building CXX object CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -MF CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o.d -o CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Msgfplus2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 94%] Linking CXX executable sqt2pin
/usr/bin/cmake -E cmake_link_script CMakeFiles/sqt2pin.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc -rdynamic CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -o sqt2pin   -L/builddir/build/BUILD/percolator-rel-3-06-04/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 -ltirpc -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
In function ‘strchr’,
    inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/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-3-06-04/converters'
[ 96%] Built target sqt2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
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make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/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/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -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-3-06-04/src/converters/Tandem2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/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 -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc -rdynamic CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -o msgf2pin   -L/builddir/build/BUILD/percolator-rel-3-06-04/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 -ltirpc -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
In function ‘strchr’,
    inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/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-3-06-04/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[100%] Built target msgf2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/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 -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated-declarations -D_GLIBCXX_PARALLEL -fopenmp -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro   -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc -rdynamic CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -o tandem2pin   -L/builddir/build/BUILD/percolator-rel-3-06-04/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 -ltirpc -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
In function ‘strchr’,
    inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/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-3-06-04/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.YZ4wsl
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x
++ dirname /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-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-3-06-04
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x 'INSTALL=/usr/bin/install -p' -C percolator
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04 -B/builddir/build/BUILD/percolator-rel-3-06-04/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/percolator//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Nothing to be done for 'src/CMakeFiles/perclibrary.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 54%] 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-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/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-3-06-04/percolator'
[ 68%] 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-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas/CMakeFiles/blas.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Nothing to be done for 'src/blas/CMakeFiles/blas.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 75%] 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-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Nothing to be done for 'src/fido/CMakeFiles/fido.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 84%] 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-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Nothing to be done for 'src/CMakeFiles/percolator.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 87%] 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-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/percolator'
make[2]: Nothing to be done for 'src/qvality/CMakeFiles/qvality.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 89%] Built target qvality
/usr/bin/make  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[100%] Built target gtest_unit
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/bin/percolator
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/bin/qvality
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/./bin/gtest_unit
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x 'INSTALL=/usr/bin/install -p' -C converters
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -B/builddir/build/BUILD/percolator-rel-3-06-04/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/converters//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/perclibrary_part.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 25%] 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-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 28%] 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-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/converters.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/converters.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 57%] 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-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/converters'
make[2]: Nothing to be done for 'MSToolkit/RAMP/CMakeFiles/RAMP.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 62%] 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-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/converters'
make[2]: Nothing to be done for 'MSToolkit/CMakeFiles/MSToolkit.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/msgf2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/sqt2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/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-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/tandem2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/bin/msgf2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/bin/sqt2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/bin/tandem2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/percolator/xml-1-1/mzIdentML1.1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/percolator/xml-2011.12.01.1/gaml_tandem1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/percolator/xml-2011.12.01.1/tandem2011.12.01.1.xsd
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
+ mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/lib64/percolator
++ find . -type f '(' -name '*.a' ')'
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libconverters.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libperclibrary_part.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/libMSToolkit.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/RAMP/libRAMP.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./fido/libfido.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/picked_protein/libpicked_protein.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/fido/libfido.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/blas/libblas.a /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/lib64/percolator
+ rm -f /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/bin/gtest_unit
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 3.06.04-1.fc40 --unique-debug-suffix -3.06.04-1.fc40.s390x --unique-debug-src-base percolator-3.06.04-1.fc40.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/percolator-rel-3-06-04
find-debuginfo: starting
Extracting debug info from 5 files
DWARF-compressing 5 files
sepdebugcrcfix: Updated 5 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/percolator-3.06.04-1.fc40.s390x
5448 blocks
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.x5Kdkl
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=z13 -mtune=z14 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-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-3-06-04
+ mkdir -p test
+ pushd test
~/build/BUILD/percolator-rel-3-06-04/test ~/build/BUILD/percolator-rel-3-06-04
+ ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt

Pin-converter version 3.06.4, Build Date Dec  8 2023 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 e3c0f9486abe4647a2aa4b91908e95c9
Reading ../yeast-01.sqt
Reading ../yeast-01.shuffled.sqt
+ ../percolator/src/percolator -X pout.xml pin.tab
Protein decoy-prefix used is random_
All files have been read
Percolator version 3.06.4, Build Date Dec  8 2023 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 Thu Dec 14 09:50:29 2023
 on e3c0f9486abe4647a2aa4b91908e95c9
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 0.6042 cpu seconds or 1 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 10193 PSMs with q<0.01
Iteration 2:	Estimated 11236 PSMs with q<0.01
Iteration 3:	Estimated 11461 PSMs with q<0.01
Iteration 4:	Estimated 11509 PSMs with q<0.01
Iteration 5:	Estimated 11560 PSMs with q<0.01
Iteration 6:	Estimated 11576 PSMs with q<0.01
Iteration 7:	Estimated 11602 PSMs with q<0.01
Iteration 8:	Estimated 11617 PSMs with q<0.01
Iteration 9:	Estimated 11617 PSMs with q<0.01
Iteration 10:	Estimated 11616 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
-0.4835	-0.3200	-0.4134	lnrSp
 0.1414	 0.1989	 0.1695	deltLCn
 0.6622	 0.6394	 0.7524	deltCn
 0.6588	 0.6486	 0.6804	Xcorr
-0.0413	 0.0625	-0.0978	Sp
 0.0244	 0.1588	 0.2191	IonFrac
 0.8867	 0.6292	 0.4141	Mass
-0.7489	-0.3031	-0.0249	PepLen
 0.1083	 0.1800	 0.1009	Charge1
 0.0250	 0.0242	 0.0043	Charge2
-0.0471	-0.0610	-0.0250	Charge3
 1.3220	 1.2346	 1.2522	enzN
 1.3377	 1.1510	 1.1172	enzC
-1.9073	-1.7718	-1.6438	enzInt
-0.0159	-0.0088	 0.1201	lnNumSP
 0.0188	 0.0011	 0.0218	dM
 0.0044	 0.0139	 0.0016	absdM
-6.5792	-6.3779	-5.8394	m0
Found 11446 test set PSMs with q<0.01.
Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide.
Selecting pi_0=0.86749
Calculating q values.
New pi_0 estimate on final list yields 7371 target peptides with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 22.6010 cpu seconds or 13 seconds wall clock time.
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ pushd percolator
~/build/BUILD/percolator-rel-3-06-04/percolator ~/build/BUILD/percolator-rel-3-06-04
+ /usr/bin/ctest --test-dir . --output-on-failure --force-new-ctest-process -j2
Test project /builddir/build/BUILD/percolator-rel-3-06-04/percolator
    Start 1: UnitTest_Percolator_RunAllTests
1/1 Test #1: UnitTest_Percolator_RunAllTests ...   Passed    0.04 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) =   0.04 sec
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: percolator-3.06.04-1.fc40.s390x
Provides: percolator = 3.06.04-1.fc40 percolator(s390-64) = 3.06.04-1.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.2)(64bit) libc.so.6(GLIBC_2.25)(64bit) libc.so.6(GLIBC_2.28)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(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(OMP_1.0)(64bit) libgomp.so.1(OMP_3.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2)(64bit) libm.so.6(GLIBC_2.29)(64bit) libsqlite3.so.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.1)(64bit) libstdc++.so.6(CXXABI_1.3.11)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.10)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(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_3.4.32)(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-3.06.04-1.fc40.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.fNmHHs
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/doc/percolator-data
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/ReadMe.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-README /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/doc/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.bW3ojE
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/licenses/percolator-data
+ export LC_ALL=
+ LC_ALL=
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/licenses/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/license.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/licenses/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/licenses/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-data = 3.06.04-1.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-static-3.06.04-1.fc40.s390x
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.ZLbmYj
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/doc/percolator-static
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/ReadMe.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-README /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/doc/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.2HQgsg
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/licenses/percolator-static
+ export LC_ALL=
+ LC_ALL=
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/licenses/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/license.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/licenses/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x/usr/share/licenses/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-static = 3.06.04-1.fc40 percolator-static(s390-64) = 3.06.04-1.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debugsource-3.06.04-1.fc40.s390x
Provides: percolator-debugsource = 3.06.04-1.fc40 percolator-debugsource(s390-64) = 3.06.04-1.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debuginfo-3.06.04-1.fc40.s390x
Provides: debuginfo(build-id) = 0932d4bcca593ac3708322b6f4034016ef521963 debuginfo(build-id) = 315f2ee161858eb3cbf7bb92ad79e9475495d2b5 debuginfo(build-id) = 5216472b9b12aea96e1b9779f2a7ad783490624e debuginfo(build-id) = c489c4e0970767d1e5e2a18d612cbcc51299c029 debuginfo(build-id) = ee0aabab823d87250309fde22e63f204e9defa37 percolator-debuginfo = 3.06.04-1.fc40 percolator-debuginfo(s390-64) = 3.06.04-1.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: percolator-debugsource(s390-64) = 3.06.04-1.fc40
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x
Wrote: /builddir/build/RPMS/percolator-static-3.06.04-1.fc40.s390x.rpm
Wrote: /builddir/build/RPMS/percolator-3.06.04-1.fc40.s390x.rpm
Wrote: /builddir/build/RPMS/percolator-debugsource-3.06.04-1.fc40.s390x.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.06.04-1.fc40.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.06.04-1.fc40.s390x.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.oHEQ2o
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/percolator-3.06.04-1.fc40.s390x
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.BKhD82
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf /builddir/build/BUILD/percolator-rel-3-06-04-SPECPARTS
+ rm -rf percolator-rel-3-06-04 percolator-rel-3-06-04.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild percolator-3.06.04-1.fc40.src.rpm
Finish: build phase for percolator-3.06.04-1.fc40.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-s390x-1702546936.417971/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-s390x-1702546936.417971/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-s390x-1702546936.417971/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/percolator-3.06.04-1.fc40.src.rpm) Config(child) 6 minutes 47 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "percolator-debugsource",
            "epoch": null,
            "version": "3.06.04",
            "release": "1.fc40",
            "arch": "s390x"
        },
        {
            "name": "percolator",
            "epoch": null,
            "version": "3.06.04",
            "release": "1.fc40",
            "arch": "src"
        },
        {
            "name": "percolator-data",
            "epoch": null,
            "version": "3.06.04",
            "release": "1.fc40",
            "arch": "noarch"
        },
        {
            "name": "percolator-debuginfo",
            "epoch": null,
            "version": "3.06.04",
            "release": "1.fc40",
            "arch": "s390x"
        },
        {
            "name": "percolator",
            "epoch": null,
            "version": "3.06.04",
            "release": "1.fc40",
            "arch": "s390x"
        },
        {
            "name": "percolator-static",
            "epoch": null,
            "version": "3.06.04",
            "release": "1.fc40",
            "arch": "s390x"
        }
    ]
}
RPMResults finished