Warning: Permanently added '13.121.81.162' (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/8425720-fedora-rawhide-s390x --chroot fedora-rawhide-s390x


Version: 1.2
PID: 8701
Logging PID: 8702
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': True,
 'build_id': 8425720,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-s390x',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '8d4a914cc97f66bf0ebc9e98e2e65f3401b339ff',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3/percolator',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'percolator',
 'package_version': '3.06.04-5',
 'project_dirname': 'gcc-15-smoketest-3',
 'project_name': 'gcc-15-smoketest-3',
 'project_owner': 'dmalcolm',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/dmalcolm/gcc-15-smoketest-3/fedora-rawhide-s390x/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None},
           {'baseurl': 'https://fedorapeople.org/~dmalcolm/gcc/gcc-15-mass-prebuild/$basearch',
            'id': 'https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch',
            'name': 'Additional repo https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch'}],
 'sandbox': 'dmalcolm/gcc-15-smoketest-3--dmalcolm',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'storage': 0,
 'submitter': 'dmalcolm',
 'tags': [],
 'task_id': '8425720-fedora-rawhide-s390x',
 'timeout': 115200,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3/percolator /var/lib/copr-rpmbuild/workspace/workdir-zsjc34sm/percolator --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/dmalcolm/gcc-15-smoketest-3/percolator', '/var/lib/copr-rpmbuild/workspace/workdir-zsjc34sm/percolator', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-zsjc34sm/percolator'...

Running: git checkout 8d4a914cc97f66bf0ebc9e98e2e65f3401b339ff --

cmd: ['git', 'checkout', '8d4a914cc97f66bf0ebc9e98e2e65f3401b339ff', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-zsjc34sm/percolator
rc: 0
stdout: 
stderr: Note: switching to '8d4a914cc97f66bf0ebc9e98e2e65f3401b339ff'.

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 8d4a914 automatic import of percolator

Running: dist-git-client sources

cmd: ['dist-git-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-zsjc34sm/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/dmalcolm/gcc-15-smoketest-3/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  4996k      0  0:00:01  0:00:01 --:--:-- 4997k
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/dmalcolm/gcc-15-smoketest-3/percolator/yeast-01.sqt.tar.gz/md5/81e1997e1c1c193cbfcd4eb54c706af9/yeast-01.sqt.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 47.9M  100 47.9M    0     0  17.8M      0  0:00:02  0:00:02 --:--:-- 17.8M
INFO: Reading stdout from command: md5sum yeast-01.sqt.tar.gz

/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-zsjc34sm/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-zsjc34sm/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1735115967.112094 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 6.0 starting (python version = 3.13.0, NVR = mock-6.0-1.fc41), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-zsjc34sm/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-zsjc34sm/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1735115967.112094 -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-zsjc34sm/percolator/percolator.spec)  Config(fedora-rawhide-s390x)
Start: clean chroot
Finish: clean chroot
Mock Version: 6.0
INFO: Mock Version: 6.0
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1735115967.112094/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 container image: registry.fedoraproject.org/fedora:rawhide
INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide
INFO: Tagging container image as mock-bootstrap-a2099b25-b3b5-4f5c-8439-ae14f7e0df01
INFO: Checking that 3b7b960754de25a7b5d910095564cdeb6486a6f173233c5c9d36ae34ad7675af image matches host's architecture
INFO: Copy content of container 3b7b960754de25a7b5d910095564cdeb6486a6f173233c5c9d36ae34ad7675af to /var/lib/mock/fedora-rawhide-s390x-bootstrap-1735115967.112094/root
INFO: mounting 3b7b960754de25a7b5d910095564cdeb6486a6f173233c5c9d36ae34ad7675af with podman image mount
INFO: image 3b7b960754de25a7b5d910095564cdeb6486a6f173233c5c9d36ae34ad7675af as /var/lib/containers/storage/overlay/b9a3c3dc0226e3eb9238d4e612f4e94d9ad0bff832af1d98b7d9b65f4d4ec7db/merged
INFO: umounting image 3b7b960754de25a7b5d910095564cdeb6486a6f173233c5c9d36ae34ad7675af (/var/lib/containers/storage/overlay/b9a3c3dc0226e3eb9238d4e612f4e94d9ad0bff832af1d98b7d9b65f4d4ec7db/merged) with podman image umount
INFO: Removing image mock-bootstrap-a2099b25-b3b5-4f5c-8439-ae14f7e0df01
INFO: Package manager dnf5 detected and used (fallback)
INFO: Not updating bootstrap chroot, bootstrap_image_ready=True
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-1735115967.112094/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 dnf5 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.20.0-1.fc42.s390x
  rpm-sequoia-1.7.0-3.fc42.s390x
  dnf5-5.2.8.1-2.fc42.s390x
  dnf5-plugins-5.2.8.1-2.fc42.s390x
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 fedora                                 100% |   6.7 MiB/s |  19.9 MiB |  00m03s
 Copr repository                        100% |   3.9 MiB/s |   6.1 MiB |  00m02s
 Additional repo https_fedorapeople_org 100% |  19.3 KiB/s |  15.6 KiB |  00m01s
Repositories loaded.
Package                            Arch   Version                    Repository                                                             Size
Installing group/module packages:
 bash                              s390x  5.2.37-1.fc42              fedora                                                              8.4 MiB
 bzip2                             s390x  1.0.8-19.fc42              copr_base                                                          84.4 KiB
 coreutils                         s390x  9.5-11.fc42                fedora                                                              5.7 MiB
 cpio                              s390x  2.15-2.fc41                fedora                                                              1.1 MiB
 diffutils                         s390x  3.10-8.fc42                copr_base                                                           1.6 MiB
 fedora-release-common             noarch 42-0.11                    fedora                                                             19.8 KiB
 findutils                         s390x  1:4.10.0-4.fc42            copr_base                                                           1.9 MiB
 gawk                              s390x  5.3.0-4.fc41               fedora                                                              1.8 MiB
 glibc-minimal-langpack            s390x  2.40.9000-24.fc42          copr_base                                                           0.0   B
 grep                              s390x  3.11-9.fc42                copr_base                                                           1.0 MiB
 gzip                              s390x  1.13-2.fc42                copr_base                                                         394.6 KiB
 info                              s390x  7.1.1-2.fc42               fedora                                                            409.1 KiB
 patch                             s390x  2.7.6-25.fc42              copr_base                                                         286.9 KiB
 redhat-rpm-config                 noarch 300-1.no_annobin.0.fc42    copr_base                                                         186.6 KiB
 rpm-build                         s390x  4.20.0-1.fc42              fedora                                                            200.4 KiB
 sed                               s390x  4.9-3.fc41                 fedora                                                            873.2 KiB
 shadow-utils                      s390x  2:4.17.0~rc1-2.fc42        fedora                                                              4.0 MiB
 tar                               s390x  2:1.35-4.fc41              fedora                                                              3.0 MiB
 unzip                             s390x  6.0-65.fc42                fedora                                                              2.2 MiB
 util-linux                        s390x  2.40.2-8.fc42              fedora                                                              3.7 MiB
 which                             s390x  2.21-42.fc41               fedora                                                             83.9 KiB
 xz                                s390x  1:5.6.3-2.fc42             fedora                                                              1.2 MiB
Installing dependencies:
 add-determinism                   s390x  0.5.0-1.fc42               fedora                                                              3.3 MiB
 alternatives                      s390x  1.31-1.fc42                fedora                                                             60.6 KiB
 ansible-srpm-macros               noarch 1-16.fc41                  fedora                                                             35.7 KiB
 audit-libs                        s390x  4.0.2-1.fc42               copr_base                                                         342.9 KiB
 authselect                        s390x  1.5.0-8.fc42               copr_base                                                         151.8 KiB
 authselect-libs                   s390x  1.5.0-8.fc42               copr_base                                                         817.4 KiB
 basesystem                        noarch 11-21.fc41                 fedora                                                              0.0   B
 binutils                          s390x  2.43.50-9.fc42             copr_base                                                          26.9 MiB
 build-reproducibility-srpm-macros noarch 0.5.0-1.fc42               fedora                                                            735.0   B
 bzip2-libs                        s390x  1.0.8-19.fc42              copr_base                                                          82.9 KiB
 ca-certificates                   noarch 2024.2.69_v8.0.401-4.fc42  fedora                                                              2.6 MiB
 coreutils-common                  s390x  9.5-11.fc42                fedora                                                             11.2 MiB
 cracklib                          s390x  2.9.11-6.fc42              copr_base                                                         225.2 KiB
 crypto-policies                   noarch 20241128-1.gitbb7b0b0.fc42 fedora                                                            137.3 KiB
 curl                              s390x  8.11.1-2.fc42              copr_base                                                         475.8 KiB
 cyrus-sasl-lib                    s390x  2.1.28-27.fc41             fedora                                                              2.4 MiB
 debugedit                         s390x  5.1-2.fc42                 copr_base                                                         193.2 KiB
 dwz                               s390x  0.15-8.fc42                copr_base                                                         307.5 KiB
 ed                                s390x  1.20.2-2.fc41              fedora                                                            150.6 KiB
 efi-srpm-macros                   noarch 5-13.fc42                  fedora                                                             40.2 KiB
 elfutils                          s390x  0.192-7.fc42               copr_base                                                           2.9 MiB
 elfutils-debuginfod-client        s390x  0.192-7.fc42               copr_base                                                          73.0 KiB
 elfutils-default-yama-scope       noarch 0.192-7.fc42               copr_base                                                           1.8 KiB
 elfutils-libelf                   s390x  0.192-7.fc42               copr_base                                                           1.2 MiB
 elfutils-libs                     s390x  0.192-7.fc42               copr_base                                                         746.5 KiB
 fedora-gpg-keys                   noarch 42-0.3                     fedora                                                            126.4 KiB
 fedora-release                    noarch 42-0.11                    fedora                                                              0.0   B
 fedora-release-identity-basic     noarch 42-0.11                    fedora                                                            719.0   B
 fedora-repos                      noarch 42-0.3                     fedora                                                              4.9 KiB
 fedora-repos-rawhide              noarch 42-0.3                     fedora                                                              2.2 KiB
 file                              s390x  5.45-8.fc42                fedora                                                             99.3 KiB
 file-libs                         s390x  5.45-8.fc42                fedora                                                              9.9 MiB
 filesystem                        s390x  3.18-29.fc42               fedora                                                            106.0   B
 filesystem-srpm-macros            noarch 3.18-29.fc42               fedora                                                             36.1 KiB
 fonts-srpm-macros                 noarch 1:2.0.5-17.fc41            fedora                                                             55.8 KiB
 forge-srpm-macros                 noarch 0.4.0-1.fc42               fedora                                                             38.9 KiB
 fpc-srpm-macros                   noarch 1.3-13.fc41                fedora                                                            144.0   B
 gdb-minimal                       s390x  15.2-4.fc42                copr_base                                                          14.7 MiB
 gdbm                              s390x  1:1.23-7.fc41              fedora                                                            483.9 KiB
 gdbm-libs                         s390x  1:1.23-7.fc41              fedora                                                            133.4 KiB
 ghc-srpm-macros                   noarch 1.9.2-1.fc42               fedora                                                            779.0   B
 glibc                             s390x  2.40.9000-24.fc42          copr_base                                                           4.9 MiB
 glibc-common                      s390x  2.40.9000-24.fc42          copr_base                                                           1.1 MiB
 glibc-gconv-extra                 s390x  2.40.9000-24.fc42          copr_base                                                           6.5 MiB
 gmp                               s390x  1:6.3.0-2.fc41             fedora                                                            770.0 KiB
 gnat-srpm-macros                  noarch 6-6.fc41                   fedora                                                              1.0 KiB
 go-srpm-macros                    noarch 3.6.0-5.fc42               fedora                                                             60.8 KiB
 jansson                           s390x  2.14-1.fc42                copr_base                                                          86.6 KiB
 json-c                            s390x  0.18-1.fc42                copr_base                                                          79.5 KiB
 kernel-srpm-macros                noarch 1.0-24.fc41                fedora                                                              1.9 KiB
 keyutils-libs                     s390x  1.6.3-4.fc42               copr_base                                                          48.6 KiB
 krb5-libs                         s390x  1.21.3-3.fc42              copr_base                                                           2.4 MiB
 libacl                            s390x  2.3.2-2.fc42               copr_base                                                          34.1 KiB
 libarchive                        s390x  3.7.7-1.fc42               copr_base                                                           1.0 MiB
 libattr                           s390x  2.5.2-4.fc41               fedora                                                             28.3 KiB
 libblkid                          s390x  2.40.2-8.fc42              fedora                                                            286.4 KiB
 libbrotli                         s390x  1.1.0-5.fc42               copr_base                                                         903.7 KiB
 libcap                            s390x  2.71-1.fc42                copr_base                                                         201.3 KiB
 libcap-ng                         s390x  0.8.5-3.fc42               copr_base                                                          58.3 KiB
 libcom_err                        s390x  1.47.1-6.fc42              fedora                                                             67.0 KiB
 libcurl                           s390x  8.11.1-2.fc42              copr_base                                                         857.0 KiB
 libeconf                          s390x  0.7.5-1.fc42               copr_base                                                          62.5 KiB
 libevent                          s390x  2.1.12-14.fc42             copr_base                                                         898.3 KiB
 libfdisk                          s390x  2.40.2-8.fc42              fedora                                                            394.8 KiB
 libffi                            s390x  3.4.6-3.fc42               fedora                                                             65.9 KiB
 libgcc                            s390x  15.0.0-0.2.fc42            https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 166.7 KiB
 libgomp                           s390x  15.0.0-0.2.fc42            https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 529.0 KiB
 libidn2                           s390x  2.3.7-2.fc42               copr_base                                                         323.5 KiB
 libmount                          s390x  2.40.2-8.fc42              fedora                                                            375.8 KiB
 libnghttp2                        s390x  1.64.0-1.fc42              fedora                                                            177.9 KiB
 libpkgconf                        s390x  2.3.0-1.fc42               fedora                                                             85.9 KiB
 libpsl                            s390x  0.21.5-4.fc42              copr_base                                                          71.1 KiB
 libpwquality                      s390x  1.4.5-11.fc42              copr_base                                                         396.1 KiB
 libselinux                        s390x  3.8-0.rc3.1.fc42           fedora                                                            203.4 KiB
 libsemanage                       s390x  3.8-0.rc3.1.fc42           fedora                                                            305.1 KiB
 libsepol                          s390x  3.8-0.rc3.1.fc42           fedora                                                            840.1 KiB
 libsmartcols                      s390x  2.40.2-8.fc42              fedora                                                            192.2 KiB
 libssh                            s390x  0.11.1-1.fc42              copr_base                                                         571.6 KiB
 libssh-config                     noarch 0.11.1-1.fc42              copr_base                                                         277.0   B
 libstdc++                         s390x  15.0.0-0.2.fc42            https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch   3.1 MiB
 libtasn1                          s390x  4.19.0-9.fc42              copr_base                                                         181.5 KiB
 libtirpc                          s390x  1.3.6-1.fc42               fedora                                                            212.5 KiB
 libtool-ltdl                      s390x  2.5.4-1.fc42               copr_base                                                          67.9 KiB
 libunistring                      s390x  1.1-8.fc42                 copr_base                                                           1.8 MiB
 libuuid                           s390x  2.40.2-8.fc42              fedora                                                             41.2 KiB
 libverto                          s390x  0.3.2-9.fc41               fedora                                                             29.3 KiB
 libxcrypt                         s390x  4.4.36-12.fc42             fedora                                                            269.1 KiB
 libxml2                           s390x  2.12.8-2.fc42              copr_base                                                           1.8 MiB
 libzstd                           s390x  1.5.6-2.fc41               fedora                                                            875.7 KiB
 lua-libs                          s390x  5.4.7-1.fc42               fedora                                                            328.8 KiB
 lua-srpm-macros                   noarch 1-14.fc41                  fedora                                                              1.3 KiB
 lz4-libs                          s390x  1.10.0-1.fc42              copr_base                                                         195.3 KiB
 mpfr                              s390x  4.2.1-5.fc42               copr_base                                                         693.2 KiB
 ncurses-base                      noarch 6.5-2.20240629.fc41        fedora                                                            326.3 KiB
 ncurses-libs                      s390x  6.5-2.20240629.fc41        fedora                                                              1.1 MiB
 ocaml-srpm-macros                 noarch 10-3.fc41                  fedora                                                              1.9 KiB
 openblas-srpm-macros              noarch 2-18.fc41                  fedora                                                            112.0   B
 openldap                          s390x  2.6.8-6.fc42               copr_base                                                         654.5 KiB
 openssl-libs                      s390x  1:3.2.2-8.fc42             copr_base                                                           6.0 MiB
 p11-kit                           s390x  0.25.5-4.fc42              copr_base                                                           2.4 MiB
 p11-kit-trust                     s390x  0.25.5-4.fc42              copr_base                                                         456.4 KiB
 package-notes-srpm-macros         noarch 0.5-12.fc41                fedora                                                              1.6 KiB
 pam                               s390x  1.7.0-3.fc42               copr_base                                                           1.5 MiB
 pam-libs                          s390x  1.7.0-3.fc42               copr_base                                                         118.1 KiB
 pcre2                             s390x  10.44-1.fc42.1             copr_base                                                         668.2 KiB
 pcre2-syntax                      noarch 10.44-1.fc42.1             copr_base                                                         251.6 KiB
 perl-srpm-macros                  noarch 1-56.fc41                  fedora                                                            861.0   B
 pkgconf                           s390x  2.3.0-1.fc42               fedora                                                             92.4 KiB
 pkgconf-m4                        noarch 2.3.0-1.fc42               fedora                                                             14.4 KiB
 pkgconf-pkg-config                s390x  2.3.0-1.fc42               fedora                                                            988.0   B
 popt                              s390x  1.19-7.fc41                fedora                                                            144.7 KiB
 publicsuffix-list-dafsa           noarch 20240107-4.fc41            fedora                                                             67.5 KiB
 pyproject-srpm-macros             noarch 1.16.3-1.fc42              fedora                                                              1.9 KiB
 python-srpm-macros                noarch 3.13-3.fc41                fedora                                                             51.0 KiB
 qt5-srpm-macros                   noarch 5.15.15-1.fc42             fedora                                                            500.0   B
 qt6-srpm-macros                   noarch 6.8.1-4.fc42               fedora                                                            456.0   B
 readline                          s390x  8.2-11.fc42                fedora                                                            556.8 KiB
 rpm                               s390x  4.20.0-1.fc42              fedora                                                              3.1 MiB
 rpm-build-libs                    s390x  4.20.0-1.fc42              fedora                                                            218.4 KiB
 rpm-libs                          s390x  4.20.0-1.fc42              fedora                                                            813.6 KiB
 rpm-sequoia                       s390x  1.7.0-3.fc42               fedora                                                              3.2 MiB
 rust-srpm-macros                  noarch 26.3-3.fc42                fedora                                                              4.8 KiB
 setup                             noarch 2.15.0-5.fc41              fedora                                                            720.7 KiB
 sqlite-libs                       s390x  3.47.2-1.fc42              fedora                                                              1.6 MiB
 systemd-libs                      s390x  257.1-1.fc42               fedora                                                              2.2 MiB
 util-linux-core                   s390x  2.40.2-8.fc42              fedora                                                              1.5 MiB
 xxhash-libs                       s390x  0.8.2-4.fc42               fedora                                                             68.0 KiB
 xz-libs                           s390x  1:5.6.3-2.fc42             fedora                                                            226.1 KiB
 zig-srpm-macros                   noarch 1-3.fc41                   fedora                                                              1.1 KiB
 zip                               s390x  3.0-42.fc42                fedora                                                            723.1 KiB
 zlib-ng-compat                    s390x  2.2.2-1.fc42               fedora                                                            109.4 KiB
 zstd                              s390x  1.5.6-2.fc41               fedora                                                              1.8 MiB
Installing groups:
 Buildsystem building group                                                                                                                     

Transaction Summary:
 Installing:       154 packages

Total size of inbound packages is 52 MiB. Need to download 52 MiB.
After this operation, 183 MiB extra will be used (install 183 MiB, remove 0 B).
[  1/154] cpio-0:2.15-2.fc41.s390x      100% | 434.3 KiB/s | 296.6 KiB |  00m01s
[  2/154] fedora-release-common-0:42-0. 100% | 209.3 KiB/s |  23.9 KiB |  00m00s
[  3/154] coreutils-0:9.5-11.fc42.s390x 100% |   1.4 MiB/s |   1.2 MiB |  00m01s
[  4/154] info-0:7.1.1-2.fc42.s390x     100% |   1.8 MiB/s | 193.4 KiB |  00m00s
[  5/154] bash-0:5.2.37-1.fc42.s390x    100% |   1.8 MiB/s |   1.9 MiB |  00m01s
[  6/154] rpm-build-0:4.20.0-1.fc42.s39 100% | 816.9 KiB/s |  83.3 KiB |  00m00s
[  7/154] sed-0:4.9-3.fc41.s390x        100% |   2.7 MiB/s | 320.2 KiB |  00m00s
[  8/154] gawk-0:5.3.0-4.fc41.s390x     100% |   3.2 MiB/s |   1.1 MiB |  00m00s
[  9/154] shadow-utils-2:4.17.0~rc1-2.f 100% |   6.3 MiB/s |   1.3 MiB |  00m00s
[ 10/154] tar-2:1.35-4.fc41.s390x       100% |   7.5 MiB/s | 877.7 KiB |  00m00s
[ 11/154] unzip-0:6.0-65.fc42.s390x     100% |   1.7 MiB/s | 195.1 KiB |  00m00s
[ 12/154] util-linux-0:2.40.2-8.fc42.s3 100% |  11.0 MiB/s |   1.1 MiB |  00m00s
[ 13/154] which-0:2.21-42.fc41.s390x    100% | 380.6 KiB/s |  43.0 KiB |  00m00s
[ 14/154] xz-1:5.6.3-2.fc42.s390x       100% |   3.8 MiB/s | 476.3 KiB |  00m00s
[ 15/154] bzip2-0:1.0.8-19.fc42.s390x   100% | 413.6 KiB/s |  50.9 KiB |  00m00s
[ 16/154] glibc-minimal-langpack-0:2.40 100% |   1.6 MiB/s | 122.4 KiB |  00m00s
[ 17/154] diffutils-0:3.10-8.fc42.s390x 100% |   1.9 MiB/s | 403.3 KiB |  00m00s
[ 18/154] findutils-1:4.10.0-4.fc42.s39 100% |   2.5 MiB/s | 542.8 KiB |  00m00s
[ 19/154] grep-0:3.11-9.fc42.s390x      100% |   2.8 MiB/s | 292.5 KiB |  00m00s
[ 20/154] gzip-0:1.13-2.fc42.s390x      100% |   1.6 MiB/s | 169.1 KiB |  00m00s
[ 21/154] patch-0:2.7.6-25.fc42.s390x   100% |   1.5 MiB/s | 136.7 KiB |  00m00s
[ 22/154] redhat-rpm-config-0:300-1.no_ 100% |   1.2 MiB/s |  76.6 KiB |  00m00s
[ 23/154] ncurses-libs-0:6.5-2.20240629 100% |   3.4 MiB/s | 360.6 KiB |  00m00s
[ 24/154] gmp-1:6.3.0-2.fc41.s390x      100% |   3.1 MiB/s | 326.3 KiB |  00m00s
[ 25/154] filesystem-0:3.18-29.fc42.s39 100% |   4.8 MiB/s |   1.1 MiB |  00m00s
[ 26/154] libattr-0:2.5.2-4.fc41.s390x  100% | 180.8 KiB/s |  18.4 KiB |  00m00s
[ 27/154] systemd-libs-0:257.1-1.fc42.s 100% |   6.7 MiB/s | 787.6 KiB |  00m00s
[ 28/154] coreutils-common-0:9.5-11.fc4 100% |   6.2 MiB/s |   2.1 MiB |  00m00s
[ 29/154] fedora-repos-0:42-0.3.noarch  100% |  90.1 KiB/s |   9.2 KiB |  00m00s
[ 30/154] readline-0:8.2-11.fc42.s390x  100% |   2.0 MiB/s | 229.7 KiB |  00m00s
[ 31/154] file-0:5.45-8.fc42.s390x      100% | 432.2 KiB/s |  48.8 KiB |  00m00s
[ 32/154] pkgconf-pkg-config-0:2.3.0-1. 100% |  97.3 KiB/s |   9.9 KiB |  00m00s
[ 33/154] popt-0:1.19-7.fc41.s390x      100% | 606.1 KiB/s |  68.5 KiB |  00m00s
[ 34/154] rpm-0:4.20.0-1.fc42.s390x     100% |   4.2 MiB/s | 546.1 KiB |  00m00s
[ 35/154] rpm-build-libs-0:4.20.0-1.fc4 100% | 985.3 KiB/s | 100.5 KiB |  00m00s
[ 36/154] rpm-libs-0:4.20.0-1.fc42.s390 100% |   2.8 MiB/s | 324.6 KiB |  00m00s
[ 37/154] zstd-0:1.5.6-2.fc41.s390x     100% |   4.4 MiB/s | 517.6 KiB |  00m00s
[ 38/154] libxcrypt-0:4.4.36-12.fc42.s3 100% |   1.2 MiB/s | 121.3 KiB |  00m00s
[ 39/154] setup-0:2.15.0-5.fc41.noarch  100% |   1.3 MiB/s | 154.4 KiB |  00m00s
[ 40/154] libfdisk-0:2.40.2-8.fc42.s390 100% |   1.6 MiB/s | 165.6 KiB |  00m00s
[ 41/154] libblkid-0:2.40.2-8.fc42.s390 100% |   1.1 MiB/s | 130.8 KiB |  00m00s
[ 42/154] libmount-0:2.40.2-8.fc42.s390 100% |   1.4 MiB/s | 159.7 KiB |  00m00s
[ 43/154] libsmartcols-0:2.40.2-8.fc42. 100% | 843.3 KiB/s |  86.0 KiB |  00m00s
[ 44/154] libuuid-0:2.40.2-8.fc42.s390x 100% | 258.8 KiB/s |  29.2 KiB |  00m00s
[ 45/154] util-linux-core-0:2.40.2-8.fc 100% |   4.7 MiB/s | 543.8 KiB |  00m00s
[ 46/154] zlib-ng-compat-0:2.2.2-1.fc42 100% | 647.4 KiB/s |  66.0 KiB |  00m00s
[ 47/154] xz-libs-1:5.6.3-2.fc42.s390x  100% |   1.0 MiB/s | 118.1 KiB |  00m00s
[ 48/154] ansible-srpm-macros-0:1-16.fc 100% | 203.7 KiB/s |  20.8 KiB |  00m00s
[ 49/154] ed-0:1.20.2-2.fc41.s390x      100% | 737.4 KiB/s |  83.3 KiB |  00m00s
[ 50/154] build-reproducibility-srpm-ma 100% | 101.5 KiB/s |  11.5 KiB |  00m00s
[ 51/154] efi-srpm-macros-0:5-13.fc42.n 100% | 220.2 KiB/s |  22.5 KiB |  00m00s
[ 52/154] filesystem-srpm-macros-0:3.18 100% | 211.1 KiB/s |  23.9 KiB |  00m00s
[ 53/154] fonts-srpm-macros-1:2.0.5-17. 100% | 236.6 KiB/s |  27.0 KiB |  00m00s
[ 54/154] forge-srpm-macros-0:0.4.0-1.f 100% | 193.7 KiB/s |  19.8 KiB |  00m00s
[ 55/154] fpc-srpm-macros-0:1.3-13.fc41 100% |  70.5 KiB/s |   8.0 KiB |  00m00s
[ 56/154] ghc-srpm-macros-0:1.9.2-1.fc4 100% |  80.7 KiB/s |   9.1 KiB |  00m00s
[ 57/154] gnat-srpm-macros-0:6-6.fc41.n 100% |  87.8 KiB/s |   9.0 KiB |  00m00s
[ 58/154] go-srpm-macros-0:3.6.0-5.fc42 100% | 247.4 KiB/s |  28.0 KiB |  00m00s
[ 59/154] kernel-srpm-macros-0:1.0-24.f 100% |  87.3 KiB/s |   9.9 KiB |  00m00s
[ 60/154] lua-srpm-macros-0:1-14.fc41.n 100% |  87.0 KiB/s |   8.9 KiB |  00m00s
[ 61/154] ocaml-srpm-macros-0:10-3.fc41 100% |  81.4 KiB/s |   9.2 KiB |  00m00s
[ 62/154] openblas-srpm-macros-0:2-18.f 100% |  68.3 KiB/s |   7.7 KiB |  00m00s
[ 63/154] package-notes-srpm-macros-0:0 100% |  96.4 KiB/s |   9.8 KiB |  00m00s
[ 64/154] perl-srpm-macros-0:1-56.fc41. 100% |  75.3 KiB/s |   8.5 KiB |  00m00s
[ 65/154] pyproject-srpm-macros-0:1.16. 100% | 121.6 KiB/s |  13.9 KiB |  00m00s
[ 66/154] python-srpm-macros-0:3.13-3.f 100% | 232.6 KiB/s |  23.7 KiB |  00m00s
[ 67/154] qt5-srpm-macros-0:5.15.15-1.f 100% |  78.7 KiB/s |   8.9 KiB |  00m00s
[ 68/154] rust-srpm-macros-0:26.3-3.fc4 100% | 118.6 KiB/s |  12.1 KiB |  00m00s
[ 69/154] qt6-srpm-macros-0:6.8.1-4.fc4 100% |  82.0 KiB/s |   9.3 KiB |  00m00s
[ 70/154] zig-srpm-macros-0:1-3.fc41.no 100% |  71.9 KiB/s |   8.1 KiB |  00m00s
[ 71/154] zip-0:3.0-42.fc42.s390x       100% |   2.6 MiB/s | 274.7 KiB |  00m00s
[ 72/154] ncurses-base-0:6.5-2.20240629 100% | 775.1 KiB/s |  88.4 KiB |  00m00s
[ 73/154] fedora-gpg-keys-0:42-0.3.noar 100% |   1.2 MiB/s | 133.6 KiB |  00m00s
[ 74/154] fedora-repos-rawhide-0:42-0.3 100% |  85.9 KiB/s |   8.8 KiB |  00m00s
[ 75/154] file-libs-0:5.45-8.fc42.s390x 100% |   6.5 MiB/s | 768.6 KiB |  00m00s
[ 76/154] pkgconf-m4-0:2.3.0-1.fc42.noa 100% | 140.4 KiB/s |  14.3 KiB |  00m00s
[ 77/154] pkgconf-0:2.3.0-1.fc42.s390x  100% | 405.7 KiB/s |  45.8 KiB |  00m00s
[ 78/154] lua-libs-0:5.4.7-1.fc42.s390x 100% |   1.2 MiB/s | 141.9 KiB |  00m00s
[ 79/154] libzstd-0:1.5.6-2.fc41.s390x  100% |   3.3 MiB/s | 346.9 KiB |  00m00s
[ 80/154] rpm-sequoia-0:1.7.0-3.fc42.s3 100% |   8.4 MiB/s | 988.6 KiB |  00m00s
[ 81/154] sqlite-libs-0:3.47.2-1.fc42.s 100% |   6.4 MiB/s | 755.2 KiB |  00m00s
[ 82/154] add-determinism-0:0.5.0-1.fc4 100% |  10.0 MiB/s |   1.0 MiB |  00m00s
[ 83/154] dwz-0:0.15-8.fc42.s390x       100% |   2.2 MiB/s | 141.4 KiB |  00m00s
[ 84/154] libpkgconf-0:2.3.0-1.fc42.s39 100% | 345.1 KiB/s |  39.0 KiB |  00m00s
[ 85/154] basesystem-0:11-21.fc41.noarc 100% |  72.3 KiB/s |   7.4 KiB |  00m00s
[ 86/154] glibc-0:2.40.9000-24.fc42.s39 100% |  14.6 MiB/s |   1.8 MiB |  00m00s
[ 87/154] libselinux-0:3.8-0.rc3.1.fc42 100% | 839.4 KiB/s |  94.9 KiB |  00m00s
[ 88/154] pcre2-0:10.44-1.fc42.1.s390x  100% |   4.0 MiB/s | 255.7 KiB |  00m00s
[ 89/154] pcre2-syntax-0:10.44-1.fc42.1 100% |   2.4 MiB/s | 150.4 KiB |  00m00s
[ 90/154] libsepol-0:3.8-0.rc3.1.fc42.s 100% |   3.2 MiB/s | 337.8 KiB |  00m00s
[ 91/154] glibc-common-0:2.40.9000-24.f 100% |   5.8 MiB/s | 407.8 KiB |  00m00s
[ 92/154] bzip2-libs-0:1.0.8-19.fc42.s3 100% |   1.5 MiB/s |  47.1 KiB |  00m00s
[ 93/154] elfutils-libelf-0:0.192-7.fc4 100% |   2.8 MiB/s | 210.7 KiB |  00m00s
[ 94/154] lz4-libs-0:1.10.0-1.fc42.s390 100% |   1.5 MiB/s |  93.5 KiB |  00m00s
[ 95/154] audit-libs-0:4.0.2-1.fc42.s39 100% |   2.0 MiB/s | 124.7 KiB |  00m00s
[ 96/154] authselect-libs-0:1.5.0-8.fc4 100% |   3.2 MiB/s | 202.0 KiB |  00m00s
[ 97/154] libcap-ng-0:0.8.5-3.fc42.s390 100% |   1.0 MiB/s |  31.4 KiB |  00m00s
[ 98/154] pam-0:1.7.0-3.fc42.s390x      100% |   7.3 MiB/s | 475.8 KiB |  00m00s
[ 99/154] gdbm-1:1.23-7.fc41.s390x      100% |   1.3 MiB/s | 155.4 KiB |  00m00s
[100/154] libgcc-0:15.0.0-0.2.fc42.s390 100% | 109.2 KiB/s |  64.4 KiB |  00m01s
[101/154] gdbm-libs-1:1.23-7.fc41.s390x 100% | 513.2 KiB/s |  58.0 KiB |  00m00s
[102/154] libtirpc-0:1.3.6-1.fc42.s390x 100% | 945.4 KiB/s |  96.4 KiB |  00m00s
[103/154] libcom_err-0:1.47.1-6.fc42.s3 100% | 234.2 KiB/s |  26.5 KiB |  00m00s
[104/154] pam-libs-0:1.7.0-3.fc42.s390x 100% |   1.8 MiB/s |  55.7 KiB |  00m00s
[105/154] libacl-0:2.3.2-2.fc42.s390x   100% | 804.6 KiB/s |  24.1 KiB |  00m00s
[106/154] libeconf-0:0.7.5-1.fc42.s390x 100% |   1.1 MiB/s |  35.0 KiB |  00m00s
[107/154] libcap-0:2.71-1.fc42.s390x    100% |   1.3 MiB/s |  81.3 KiB |  00m00s
[108/154] openssl-libs-1:3.2.2-8.fc42.s 100% |  23.1 MiB/s |   1.9 MiB |  00m00s
[109/154] libsemanage-0:3.8-0.rc3.1.fc4 100% |   1.0 MiB/s | 116.8 KiB |  00m00s
[110/154] crypto-policies-0:20241128-1. 100% | 870.4 KiB/s |  98.4 KiB |  00m00s
[111/154] libstdc++-0:15.0.0-0.2.fc42.s 100% | 970.7 KiB/s | 905.6 KiB |  00m01s
[112/154] ca-certificates-0:2024.2.69_v 100% |   4.5 MiB/s | 948.9 KiB |  00m00s
[113/154] elfutils-libs-0:0.192-7.fc42. 100% |   4.4 MiB/s | 273.8 KiB |  00m00s
[114/154] libffi-0:3.4.6-3.fc42.s390x   100% | 318.2 KiB/s |  36.0 KiB |  00m00s
[115/154] binutils-0:2.43.50-9.fc42.s39 100% |  49.3 MiB/s |   5.9 MiB |  00m00s
[116/154] debugedit-0:5.1-2.fc42.s390x  100% | 896.2 KiB/s |  78.9 KiB |  00m00s
[117/154] elfutils-0:0.192-7.fc42.s390x 100% |   8.6 MiB/s | 543.9 KiB |  00m00s
[118/154] libarchive-0:3.7.7-1.fc42.s39 100% |   6.7 MiB/s | 433.7 KiB |  00m00s
[119/154] curl-0:8.11.1-2.fc42.s390x    100% |   3.6 MiB/s | 224.0 KiB |  00m00s
[120/154] krb5-libs-0:1.21.3-3.fc42.s39 100% |  11.7 MiB/s | 742.7 KiB |  00m00s
[121/154] mpfr-0:4.2.1-5.fc42.s390x     100% |   4.7 MiB/s | 295.1 KiB |  00m00s
[122/154] libverto-0:0.3.2-9.fc41.s390x 100% | 184.7 KiB/s |  20.9 KiB |  00m00s
[123/154] p11-kit-0:0.25.5-4.fc42.s390x 100% |   7.4 MiB/s | 461.7 KiB |  00m00s
[124/154] p11-kit-trust-0:0.25.5-4.fc42 100% |   2.2 MiB/s | 135.6 KiB |  00m00s
[125/154] glibc-gconv-extra-0:2.40.9000 100% |  22.8 MiB/s |   1.5 MiB |  00m00s
[126/154] libgomp-0:15.0.0-0.2.fc42.s39 100% | 710.1 KiB/s | 332.3 KiB |  00m00s
[127/154] authselect-0:1.5.0-8.fc42.s39 100% |   2.3 MiB/s | 139.7 KiB |  00m00s
[128/154] libpwquality-0:1.4.5-11.fc42. 100% |   1.7 MiB/s | 104.8 KiB |  00m00s
[129/154] libtasn1-0:4.19.0-9.fc42.s390 100% |   1.3 MiB/s |  76.3 KiB |  00m00s
[130/154] cracklib-0:2.9.11-6.fc42.s390 100% |   1.3 MiB/s |  79.4 KiB |  00m00s
[131/154] alternatives-0:1.31-1.fc42.s3 100% | 357.8 KiB/s |  40.4 KiB |  00m00s
[132/154] keyutils-libs-0:1.6.3-4.fc42. 100% |   1.0 MiB/s |  30.3 KiB |  00m00s
[133/154] libxml2-0:2.12.8-2.fc42.s390x 100% |  10.6 MiB/s | 673.7 KiB |  00m00s
[134/154] elfutils-default-yama-scope-0 100% | 431.0 KiB/s |  12.9 KiB |  00m00s
[135/154] elfutils-debuginfod-client-0: 100% |   1.5 MiB/s |  45.2 KiB |  00m00s
[136/154] jansson-0:2.14-1.fc42.s390x   100% |   1.4 MiB/s |  43.3 KiB |  00m00s
[137/154] json-c-0:0.18-1.fc42.s390x    100% |   1.4 MiB/s |  41.8 KiB |  00m00s
[138/154] gdb-minimal-0:15.2-4.fc42.s39 100% |  45.3 MiB/s |   4.3 MiB |  00m00s
[139/154] fedora-release-0:42-0.11.noar 100% | 114.9 KiB/s |  13.0 KiB |  00m00s
[140/154] xxhash-libs-0:0.8.2-4.fc42.s3 100% | 355.3 KiB/s |  36.2 KiB |  00m00s
[141/154] libcurl-0:8.11.1-2.fc42.s390x 100% |   5.8 MiB/s | 370.7 KiB |  00m00s
[142/154] fedora-release-identity-basic 100% | 122.0 KiB/s |  13.8 KiB |  00m00s
[143/154] libnghttp2-0:1.64.0-1.fc42.s3 100% | 706.0 KiB/s |  79.8 KiB |  00m00s
[144/154] libbrotli-0:1.1.0-5.fc42.s390 100% |   6.0 MiB/s | 376.2 KiB |  00m00s
[145/154] libpsl-0:0.21.5-4.fc42.s390x  100% |   2.1 MiB/s |  63.7 KiB |  00m00s
[146/154] libidn2-0:2.3.7-2.fc42.s390x  100% |   1.8 MiB/s | 111.4 KiB |  00m00s
[147/154] libssh-0:0.11.1-1.fc42.s390x  100% |   3.6 MiB/s | 220.5 KiB |  00m00s
[148/154] openldap-0:2.6.8-6.fc42.s390x 100% |   4.1 MiB/s | 248.9 KiB |  00m00s
[149/154] publicsuffix-list-dafsa-0:202 100% | 515.7 KiB/s |  58.3 KiB |  00m00s
[150/154] libtool-ltdl-0:2.5.4-1.fc42.s 100% |   1.1 MiB/s |  35.1 KiB |  00m00s
[151/154] libevent-0:2.1.12-14.fc42.s39 100% |   4.0 MiB/s | 244.7 KiB |  00m00s
[152/154] libssh-config-0:0.11.1-1.fc42 100% | 328.4 KiB/s |   9.9 KiB |  00m00s
[153/154] libunistring-0:1.1-8.fc42.s39 100% |   8.5 MiB/s | 550.9 KiB |  00m00s
[154/154] cyrus-sasl-lib-0:2.1.28-27.fc 100% |   2.6 MiB/s | 827.5 KiB |  00m00s
--------------------------------------------------------------------------------
[154/154] Total                         100% |   7.5 MiB/s |  52.2 MiB |  00m07s
Running transaction
Importing OpenPGP key 0x105EF944:
 UserID     : "Fedora (42) <fedora-42-primary@fedoraproject.org>"
 Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary
The key was successfully imported.
Importing OpenPGP key 0x105EF944:
 UserID     : "Fedora (42) <fedora-42-primary@fedoraproject.org>"
 Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary
The key was successfully imported.
Importing OpenPGP key 0xE99D6AD1:
 UserID     : "Fedora (41) <fedora-41-primary@fedoraproject.org>"
 Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary
The key was successfully imported.
Importing OpenPGP key 0x31645531:
 UserID     : "Fedora (43) <fedora-43-primary@fedoraproject.org>"
 Fingerprint: C6E7F081CF80E13146676E88829B606631645531
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary
The key was successfully imported.
[  1/156] Verify package files          100% | 758.0   B/s | 154.0   B |  00m00s
>>> Running pre-transaction scriptlet: filesystem-0:3.18-29.fc42.s390x
>>> Finished pre-transaction scriptlet: filesystem-0:3.18-29.fc42.s390x
>>> [RPM] /var/lib/mock/fedora-rawhide-s390x-1735115967.112094/root/var/cache/dn
[  2/156] Prepare transaction           100% |   2.8 KiB/s | 154.0   B |  00m00s
[  3/156] Installing libgcc-0:15.0.0-0. 100% | 164.5 MiB/s | 168.4 KiB |  00m00s
[  4/156] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
[  5/156] Installing publicsuffix-list- 100% |   0.0   B/s |  68.3 KiB |  00m00s
[  6/156] Installing fedora-release-ide 100% |   0.0   B/s | 976.0   B |  00m00s
[  7/156] Installing fedora-repos-rawhi 100% |   0.0   B/s |   2.4 KiB |  00m00s
[  8/156] Installing fedora-gpg-keys-0: 100% |  42.0 MiB/s | 172.2 KiB |  00m00s
[  9/156] Installing fedora-repos-0:42- 100% |   0.0   B/s |   5.7 KiB |  00m00s
[ 10/156] Installing fedora-release-com 100% |  23.6 MiB/s |  24.1 KiB |  00m00s
[ 11/156] Installing fedora-release-0:4 100% |   0.0   B/s | 124.0   B |  00m00s
[ 12/156] Installing setup-0:2.15.0-5.f 100% |  50.6 MiB/s | 726.1 KiB |  00m00s
>>> [RPM] /etc/hosts created as /etc/hosts.rpmnew
[ 13/156] Installing filesystem-0:3.18- 100% |   3.1 MiB/s | 212.6 KiB |  00m00s
[ 14/156] Installing basesystem-0:11-21 100% |   0.0   B/s | 124.0   B |  00m00s
[ 15/156] Installing pcre2-syntax-0:10. 100% | 248.1 MiB/s | 254.1 KiB |  00m00s
[ 16/156] Installing pkgconf-m4-0:2.3.0 100% |   0.0   B/s |  14.8 KiB |  00m00s
[ 17/156] Installing ncurses-base-0:6.5 100% |  68.7 MiB/s | 351.7 KiB |  00m00s
[ 18/156] Installing glibc-minimal-lang 100% |   0.0   B/s | 124.0   B |  00m00s
[ 19/156] Installing ncurses-libs-0:6.5 100% | 177.1 MiB/s |   1.1 MiB |  00m00s
[ 20/156] Installing glibc-0:2.40.9000- 100% | 198.0 MiB/s |   5.0 MiB |  00m00s
[ 21/156] Installing bash-0:5.2.37-1.fc 100% | 300.1 MiB/s |   8.4 MiB |  00m00s
[ 22/156] Installing glibc-common-0:2.4 100% | 151.8 MiB/s |   1.1 MiB |  00m00s
[ 23/156] Installing glibc-gconv-extra- 100% | 207.1 MiB/s |   6.6 MiB |  00m00s
[ 24/156] Installing zlib-ng-compat-0:2 100% | 107.7 MiB/s | 110.3 KiB |  00m00s
[ 25/156] Installing xz-libs-1:5.6.3-2. 100% | 221.9 MiB/s | 227.2 KiB |  00m00s
[ 26/156] Installing bzip2-libs-0:1.0.8 100% |  82.1 MiB/s |  84.0 KiB |  00m00s
[ 27/156] Installing readline-0:8.2-11. 100% | 272.9 MiB/s | 558.9 KiB |  00m00s
[ 28/156] Installing popt-0:1.19-7.fc41 100% |  73.9 MiB/s | 151.3 KiB |  00m00s
[ 29/156] Installing libuuid-0:2.40.2-8 100% |   0.0   B/s |  42.3 KiB |  00m00s
[ 30/156] Installing libblkid-0:2.40.2- 100% | 280.8 MiB/s | 287.6 KiB |  00m00s
[ 31/156] Installing gmp-1:6.3.0-2.fc41 100% | 251.4 MiB/s | 772.2 KiB |  00m00s
[ 32/156] Installing libxcrypt-0:4.4.36 100% | 265.4 MiB/s | 271.8 KiB |  00m00s
[ 33/156] Installing libzstd-0:1.5.6-2. 100% | 214.1 MiB/s | 877.0 KiB |  00m00s
[ 34/156] Installing elfutils-libelf-0: 100% | 293.7 MiB/s |   1.2 MiB |  00m00s
[ 35/156] Installing libstdc++-0:15.0.0 100% | 279.5 MiB/s |   3.1 MiB |  00m00s
[ 36/156] Installing libattr-0:2.5.2-4. 100% |   0.0   B/s |  29.3 KiB |  00m00s
[ 37/156] Installing libacl-0:2.3.2-2.f 100% |   0.0   B/s |  34.9 KiB |  00m00s
[ 38/156] Installing gdbm-libs-1:1.23-7 100% | 132.0 MiB/s | 135.1 KiB |  00m00s
[ 39/156] Installing libeconf-0:0.7.5-1 100% |  62.6 MiB/s |  64.2 KiB |  00m00s
[ 40/156] Installing dwz-0:0.15-8.fc42. 100% | 150.8 MiB/s | 308.8 KiB |  00m00s
[ 41/156] Installing mpfr-0:4.2.1-5.fc4 100% | 226.2 MiB/s | 694.8 KiB |  00m00s
[ 42/156] Installing gawk-0:5.3.0-4.fc4 100% | 226.8 MiB/s |   1.8 MiB |  00m00s
[ 43/156] Installing unzip-0:6.0-65.fc4 100% | 552.0 MiB/s |   2.2 MiB |  00m00s
[ 44/156] Installing file-libs-0:5.45-8 100% | 497.1 MiB/s |   9.9 MiB |  00m00s
[ 45/156] Installing file-0:5.45-8.fc42 100% |  14.1 MiB/s | 100.8 KiB |  00m00s
[ 46/156] Installing crypto-policies-0: 100% |  32.0 MiB/s | 163.7 KiB |  00m00s
[ 47/156] Installing libsmartcols-0:2.4 100% | 188.7 MiB/s | 193.2 KiB |  00m00s
[ 48/156] Installing lua-libs-0:5.4.7-1 100% | 161.2 MiB/s | 330.0 KiB |  00m00s
[ 49/156] Installing libsepol-0:3.8-0.r 100% | 205.3 MiB/s | 841.0 KiB |  00m00s
[ 50/156] Installing pcre2-0:10.44-1.fc 100% | 218.0 MiB/s | 669.6 KiB |  00m00s
[ 51/156] Installing libselinux-0:3.8-0 100% | 199.9 MiB/s | 204.7 KiB |  00m00s
[ 52/156] Installing sed-0:4.9-3.fc41.s 100% | 172.1 MiB/s | 881.4 KiB |  00m00s
[ 53/156] Installing findutils-1:4.10.0 100% | 235.3 MiB/s |   1.9 MiB |  00m00s
[ 54/156] Installing grep-0:3.11-9.fc42 100% | 168.6 MiB/s |   1.0 MiB |  00m00s
[ 55/156] Installing xz-1:5.6.3-2.fc42. 100% | 177.2 MiB/s |   1.2 MiB |  00m00s
[ 56/156] Installing libmount-0:2.40.2- 100% | 184.0 MiB/s | 376.9 KiB |  00m00s
[ 57/156] Installing lz4-libs-0:1.10.0- 100% | 191.8 MiB/s | 196.4 KiB |  00m00s
[ 58/156] Installing libcap-ng-0:0.8.5- 100% |  58.8 MiB/s |  60.2 KiB |  00m00s
[ 59/156] Installing audit-libs-0:4.0.2 100% | 168.4 MiB/s | 345.0 KiB |  00m00s
[ 60/156] Installing pam-libs-0:1.7.0-3 100% | 117.7 MiB/s | 120.5 KiB |  00m00s
[ 61/156] Installing libcap-0:2.71-1.fc 100% | 100.7 MiB/s | 206.3 KiB |  00m00s
[ 62/156] Installing systemd-libs-0:257 100% | 249.5 MiB/s |   2.2 MiB |  00m00s
[ 63/156] Installing libcom_err-0:1.47. 100% |   0.0   B/s |  68.0 KiB |  00m00s
[ 64/156] Installing libffi-0:3.4.6-3.f 100% |   0.0   B/s |  67.3 KiB |  00m00s
[ 65/156] Installing alternatives-0:1.3 100% |   0.0   B/s |  62.2 KiB |  00m00s
[ 66/156] Installing libtasn1-0:4.19.0- 100% |  35.8 MiB/s | 183.3 KiB |  00m00s
[ 67/156] Installing p11-kit-0:0.25.5-4 100% | 243.7 MiB/s |   2.4 MiB |  00m00s
[ 68/156] Installing libunistring-0:1.1 100% | 251.6 MiB/s |   1.8 MiB |  00m00s
[ 69/156] Installing libidn2-0:2.3.7-2. 100% | 107.2 MiB/s | 329.4 KiB |  00m00s
[ 70/156] Installing libpsl-0:0.21.5-4. 100% |  70.5 MiB/s |  72.2 KiB |  00m00s
[ 71/156] Installing p11-kit-trust-0:0. 100% |  63.9 MiB/s | 458.1 KiB |  00m00s
[ 72/156] Installing util-linux-core-0: 100% | 192.9 MiB/s |   1.5 MiB |  00m00s
[ 73/156] Installing libsemanage-0:3.8- 100% |  99.9 MiB/s | 306.9 KiB |  00m00s
[ 74/156] Installing shadow-utils-2:4.1 100% | 176.2 MiB/s |   4.1 MiB |  00m00s
[ 75/156] Installing zstd-0:1.5.6-2.fc4 100% | 262.1 MiB/s |   1.8 MiB |  00m00s
[ 76/156] Installing tar-2:1.35-4.fc41. 100% | 274.6 MiB/s |   3.0 MiB |  00m00s
[ 77/156] Installing zip-0:3.0-42.fc42. 100% | 236.7 MiB/s | 727.0 KiB |  00m00s
[ 78/156] Installing gdbm-1:1.23-7.fc41 100% | 159.1 MiB/s | 488.8 KiB |  00m00s
[ 79/156] Installing cyrus-sasl-lib-0:2 100% | 265.4 MiB/s |   2.4 MiB |  00m00s
[ 80/156] Installing libfdisk-0:2.40.2- 100% | 193.3 MiB/s | 395.9 KiB |  00m00s
[ 81/156] Installing bzip2-0:1.0.8-19.f 100% |  86.8 MiB/s |  88.9 KiB |  00m00s
[ 82/156] Installing libxml2-0:2.12.8-2 100% | 228.7 MiB/s |   1.8 MiB |  00m00s
[ 83/156] Installing sqlite-libs-0:3.47 100% | 226.7 MiB/s |   1.6 MiB |  00m00s
[ 84/156] Installing add-determinism-0: 100% | 251.3 MiB/s |   3.3 MiB |  00m00s
[ 85/156] Installing build-reproducibil 100% |   0.0   B/s |   1.0 KiB |  00m00s
[ 86/156] Installing ed-0:1.20.2-2.fc41 100% | 149.3 MiB/s | 152.9 KiB |  00m00s
[ 87/156] Installing patch-0:2.7.6-25.f 100% | 140.8 MiB/s | 288.4 KiB |  00m00s
[ 88/156] Installing filesystem-srpm-ma 100% |   0.0   B/s |  36.8 KiB |  00m00s
[ 89/156] Installing elfutils-default-y 100% | 510.7 KiB/s |   2.0 KiB |  00m00s
[ 90/156] Installing elfutils-libs-0:0. 100% | 182.7 MiB/s | 748.4 KiB |  00m00s
[ 91/156] Installing cpio-0:2.15-2.fc41 100% | 186.5 MiB/s |   1.1 MiB |  00m00s
[ 92/156] Installing diffutils-0:3.10-8 100% | 228.2 MiB/s |   1.6 MiB |  00m00s
[ 93/156] Installing libpkgconf-0:2.3.0 100% |  84.9 MiB/s |  87.0 KiB |  00m00s
[ 94/156] Installing pkgconf-0:2.3.0-1. 100% |  92.7 MiB/s |  94.9 KiB |  00m00s
[ 95/156] Installing pkgconf-pkg-config 100% |   0.0   B/s |   1.8 KiB |  00m00s
[ 96/156] Installing libgomp-0:15.0.0-0 100% | 259.0 MiB/s | 530.4 KiB |  00m00s
[ 97/156] Installing libverto-0:0.3.2-9 100% |   0.0   B/s |  31.1 KiB |  00m00s
[ 98/156] Installing keyutils-libs-0:1. 100% |  48.8 MiB/s |  50.0 KiB |  00m00s
[ 99/156] Installing jansson-0:2.14-1.f 100% |  85.9 MiB/s |  88.0 KiB |  00m00s
[100/156] Installing json-c-0:0.18-1.fc 100% |  78.9 MiB/s |  80.8 KiB |  00m00s
[101/156] Installing xxhash-libs-0:0.8. 100% |  67.8 MiB/s |  69.4 KiB |  00m00s
[102/156] Installing libnghttp2-0:1.64. 100% | 174.9 MiB/s | 179.1 KiB |  00m00s
[103/156] Installing libbrotli-0:1.1.0- 100% | 177.0 MiB/s | 906.0 KiB |  00m00s
[104/156] Installing libtool-ltdl-0:2.5 100% |  67.4 MiB/s |  69.0 KiB |  00m00s
[105/156] Installing rust-srpm-macros-0 100% |   0.0   B/s |   5.6 KiB |  00m00s
[106/156] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 732.0   B |  00m00s
[107/156] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 776.0   B |  00m00s
[108/156] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[109/156] Installing package-notes-srpm 100% |   0.0   B/s |   2.0 KiB |  00m00s
[110/156] Installing openblas-srpm-macr 100% |   0.0   B/s | 392.0   B |  00m00s
[111/156] Installing ocaml-srpm-macros- 100% |   0.0   B/s |   2.2 KiB |  00m00s
[112/156] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[113/156] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[114/156] Installing ghc-srpm-macros-0: 100% |   0.0   B/s |   1.0 KiB |  00m00s
[115/156] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[116/156] Installing ansible-srpm-macro 100% |  35.4 MiB/s |  36.2 KiB |  00m00s
[117/156] Installing coreutils-common-0 100% | 310.8 MiB/s |  11.2 MiB |  00m00s
[118/156] Installing openssl-libs-1:3.2 100% | 259.3 MiB/s |   6.0 MiB |  00m00s
[119/156] Installing coreutils-0:9.5-11 100% | 212.1 MiB/s |   5.7 MiB |  00m00s
[120/156] Installing ca-certificates-0: 100% |   1.6 MiB/s |   2.4 MiB |  00m01s
[121/156] Installing krb5-libs-0:1.21.3 100% | 215.8 MiB/s |   2.4 MiB |  00m00s
[122/156] Installing libarchive-0:3.7.7 100% | 245.4 MiB/s |   1.0 MiB |  00m00s
[123/156] Installing gzip-0:1.13-2.fc42 100% | 195.4 MiB/s | 400.1 KiB |  00m00s
[124/156] Installing authselect-libs-0: 100% | 162.6 MiB/s | 832.3 KiB |  00m00s
[125/156] Installing cracklib-0:2.9.11- 100% |  77.0 MiB/s | 236.5 KiB |  00m00s
[126/156] Installing libpwquality-0:1.4 100% |  99.7 MiB/s | 408.5 KiB |  00m00s
[127/156] Installing libtirpc-0:1.3.6-1 100% | 104.6 MiB/s | 214.3 KiB |  00m00s
[128/156] Installing pam-0:1.7.0-3.fc42 100% | 140.7 MiB/s |   1.5 MiB |  00m00s
[129/156] Installing libssh-0:0.11.1-1. 100% | 280.1 MiB/s | 573.6 KiB |  00m00s
[130/156] Installing rpm-sequoia-0:1.7. 100% | 287.3 MiB/s |   3.2 MiB |  00m00s
[131/156] Installing rpm-libs-0:4.20.0- 100% | 265.3 MiB/s | 815.1 KiB |  00m00s
[132/156] Installing rpm-build-libs-0:4 100% | 214.1 MiB/s | 219.3 KiB |  00m00s
[133/156] Installing libevent-0:2.1.12- 100% | 293.6 MiB/s | 902.1 KiB |  00m00s
[134/156] Installing openldap-0:2.6.8-6 100% | 214.3 MiB/s | 658.3 KiB |  00m00s
[135/156] Installing libcurl-0:8.11.1-2 100% | 279.3 MiB/s | 858.1 KiB |  00m00s
[136/156] Installing elfutils-debuginfo 100% |  73.4 MiB/s |  75.2 KiB |  00m00s
[137/156] Installing binutils-0:2.43.50 100% | 320.7 MiB/s |  26.9 MiB |  00m00s
[138/156] Installing elfutils-0:0.192-7 100% | 325.6 MiB/s |   2.9 MiB |  00m00s
[139/156] Installing gdb-minimal-0:15.2 100% | 282.6 MiB/s |  14.7 MiB |  00m00s
[140/156] Installing debugedit-0:5.1-2. 100% | 191.3 MiB/s | 195.9 KiB |  00m00s
[141/156] Installing curl-0:8.11.1-2.fc 100% |  51.9 MiB/s | 478.3 KiB |  00m00s
[142/156] Installing rpm-0:4.20.0-1.fc4 100% | 167.0 MiB/s |   2.5 MiB |  00m00s
[143/156] Installing efi-srpm-macros-0: 100% |   0.0   B/s |  41.2 KiB |  00m00s
[144/156] Installing lua-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[145/156] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.7 KiB |  00m00s
[146/156] Installing fonts-srpm-macros- 100% |  55.7 MiB/s |  57.0 KiB |  00m00s
[147/156] Installing forge-srpm-macros- 100% |   0.0   B/s |  40.3 KiB |  00m00s
[148/156] Installing go-srpm-macros-0:3 100% |  60.5 MiB/s |  62.0 KiB |  00m00s
[149/156] Installing python-srpm-macros 100% |  50.9 MiB/s |  52.2 KiB |  00m00s
[150/156] Installing redhat-rpm-config- 100% |  94.3 MiB/s | 193.2 KiB |  00m00s
[151/156] Installing rpm-build-0:4.20.0 100% | 102.0 MiB/s | 209.0 KiB |  00m00s
[152/156] Installing pyproject-srpm-mac 100% |   1.2 MiB/s |   2.5 KiB |  00m00s
[153/156] Installing util-linux-0:2.40. 100% | 155.4 MiB/s |   3.7 MiB |  00m00s
[154/156] Installing authselect-0:1.5.0 100% |  76.3 MiB/s | 156.2 KiB |  00m00s
[155/156] Installing which-0:2.21-42.fc 100% |  84.1 MiB/s |  86.1 KiB |  00m00s
[156/156] Installing info-0:7.1.1-2.fc4 100% | 230.4 KiB/s | 409.5 KiB |  00m02s
Warning: skipped OpenPGP checks for 60 packages from repositories: copr_base, https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch
Complete!
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: add-determinism-0.5.0-1.fc42.s390x
alternatives-1.31-1.fc42.s390x
ansible-srpm-macros-1-16.fc41.noarch
audit-libs-4.0.2-1.fc42.s390x
authselect-1.5.0-8.fc42.s390x
authselect-libs-1.5.0-8.fc42.s390x
basesystem-11-21.fc41.noarch
bash-5.2.37-1.fc42.s390x
binutils-2.43.50-9.fc42.s390x
build-reproducibility-srpm-macros-0.5.0-1.fc42.noarch
bzip2-1.0.8-19.fc42.s390x
bzip2-libs-1.0.8-19.fc42.s390x
ca-certificates-2024.2.69_v8.0.401-4.fc42.noarch
coreutils-9.5-11.fc42.s390x
coreutils-common-9.5-11.fc42.s390x
cpio-2.15-2.fc41.s390x
cracklib-2.9.11-6.fc42.s390x
crypto-policies-20241128-1.gitbb7b0b0.fc42.noarch
curl-8.11.1-2.fc42.s390x
cyrus-sasl-lib-2.1.28-27.fc41.s390x
debugedit-5.1-2.fc42.s390x
diffutils-3.10-8.fc42.s390x
dwz-0.15-8.fc42.s390x
ed-1.20.2-2.fc41.s390x
efi-srpm-macros-5-13.fc42.noarch
elfutils-0.192-7.fc42.s390x
elfutils-debuginfod-client-0.192-7.fc42.s390x
elfutils-default-yama-scope-0.192-7.fc42.noarch
elfutils-libelf-0.192-7.fc42.s390x
elfutils-libs-0.192-7.fc42.s390x
fedora-gpg-keys-42-0.3.noarch
fedora-release-42-0.11.noarch
fedora-release-common-42-0.11.noarch
fedora-release-identity-basic-42-0.11.noarch
fedora-repos-42-0.3.noarch
fedora-repos-rawhide-42-0.3.noarch
file-5.45-8.fc42.s390x
file-libs-5.45-8.fc42.s390x
filesystem-3.18-29.fc42.s390x
filesystem-srpm-macros-3.18-29.fc42.noarch
findutils-4.10.0-4.fc42.s390x
fonts-srpm-macros-2.0.5-17.fc41.noarch
forge-srpm-macros-0.4.0-1.fc42.noarch
fpc-srpm-macros-1.3-13.fc41.noarch
gawk-5.3.0-4.fc41.s390x
gdb-minimal-15.2-4.fc42.s390x
gdbm-1.23-7.fc41.s390x
gdbm-libs-1.23-7.fc41.s390x
ghc-srpm-macros-1.9.2-1.fc42.noarch
glibc-2.40.9000-24.fc42.s390x
glibc-common-2.40.9000-24.fc42.s390x
glibc-gconv-extra-2.40.9000-24.fc42.s390x
glibc-minimal-langpack-2.40.9000-24.fc42.s390x
gmp-6.3.0-2.fc41.s390x
gnat-srpm-macros-6-6.fc41.noarch
go-srpm-macros-3.6.0-5.fc42.noarch
gpg-pubkey-105ef944-65ca83d1
gpg-pubkey-31645531-66b6dccf
gpg-pubkey-e99d6ad1-64d2612c
grep-3.11-9.fc42.s390x
gzip-1.13-2.fc42.s390x
info-7.1.1-2.fc42.s390x
jansson-2.14-1.fc42.s390x
json-c-0.18-1.fc42.s390x
kernel-srpm-macros-1.0-24.fc41.noarch
keyutils-libs-1.6.3-4.fc42.s390x
krb5-libs-1.21.3-3.fc42.s390x
libacl-2.3.2-2.fc42.s390x
libarchive-3.7.7-1.fc42.s390x
libattr-2.5.2-4.fc41.s390x
libblkid-2.40.2-8.fc42.s390x
libbrotli-1.1.0-5.fc42.s390x
libcap-2.71-1.fc42.s390x
libcap-ng-0.8.5-3.fc42.s390x
libcom_err-1.47.1-6.fc42.s390x
libcurl-8.11.1-2.fc42.s390x
libeconf-0.7.5-1.fc42.s390x
libevent-2.1.12-14.fc42.s390x
libfdisk-2.40.2-8.fc42.s390x
libffi-3.4.6-3.fc42.s390x
libgcc-15.0.0-0.2.fc42.s390x
libgomp-15.0.0-0.2.fc42.s390x
libidn2-2.3.7-2.fc42.s390x
libmount-2.40.2-8.fc42.s390x
libnghttp2-1.64.0-1.fc42.s390x
libpkgconf-2.3.0-1.fc42.s390x
libpsl-0.21.5-4.fc42.s390x
libpwquality-1.4.5-11.fc42.s390x
libselinux-3.8-0.rc3.1.fc42.s390x
libsemanage-3.8-0.rc3.1.fc42.s390x
libsepol-3.8-0.rc3.1.fc42.s390x
libsmartcols-2.40.2-8.fc42.s390x
libssh-0.11.1-1.fc42.s390x
libssh-config-0.11.1-1.fc42.noarch
libstdc++-15.0.0-0.2.fc42.s390x
libtasn1-4.19.0-9.fc42.s390x
libtirpc-1.3.6-1.fc42.s390x
libtool-ltdl-2.5.4-1.fc42.s390x
libunistring-1.1-8.fc42.s390x
libuuid-2.40.2-8.fc42.s390x
libverto-0.3.2-9.fc41.s390x
libxcrypt-4.4.36-12.fc42.s390x
libxml2-2.12.8-2.fc42.s390x
libzstd-1.5.6-2.fc41.s390x
lua-libs-5.4.7-1.fc42.s390x
lua-srpm-macros-1-14.fc41.noarch
lz4-libs-1.10.0-1.fc42.s390x
mpfr-4.2.1-5.fc42.s390x
ncurses-base-6.5-2.20240629.fc41.noarch
ncurses-libs-6.5-2.20240629.fc41.s390x
ocaml-srpm-macros-10-3.fc41.noarch
openblas-srpm-macros-2-18.fc41.noarch
openldap-2.6.8-6.fc42.s390x
openssl-libs-3.2.2-8.fc42.s390x
p11-kit-0.25.5-4.fc42.s390x
p11-kit-trust-0.25.5-4.fc42.s390x
package-notes-srpm-macros-0.5-12.fc41.noarch
pam-1.7.0-3.fc42.s390x
pam-libs-1.7.0-3.fc42.s390x
patch-2.7.6-25.fc42.s390x
pcre2-10.44-1.fc42.1.s390x
pcre2-syntax-10.44-1.fc42.1.noarch
perl-srpm-macros-1-56.fc41.noarch
pkgconf-2.3.0-1.fc42.s390x
pkgconf-m4-2.3.0-1.fc42.noarch
pkgconf-pkg-config-2.3.0-1.fc42.s390x
popt-1.19-7.fc41.s390x
publicsuffix-list-dafsa-20240107-4.fc41.noarch
pyproject-srpm-macros-1.16.3-1.fc42.noarch
python-srpm-macros-3.13-3.fc41.noarch
qt5-srpm-macros-5.15.15-1.fc42.noarch
qt6-srpm-macros-6.8.1-4.fc42.noarch
readline-8.2-11.fc42.s390x
redhat-rpm-config-300-1.no_annobin.0.fc42.noarch
rpm-4.20.0-1.fc42.s390x
rpm-build-4.20.0-1.fc42.s390x
rpm-build-libs-4.20.0-1.fc42.s390x
rpm-libs-4.20.0-1.fc42.s390x
rpm-sequoia-1.7.0-3.fc42.s390x
rust-srpm-macros-26.3-3.fc42.noarch
sed-4.9-3.fc41.s390x
setup-2.15.0-5.fc41.noarch
shadow-utils-4.17.0~rc1-2.fc42.s390x
sqlite-libs-3.47.2-1.fc42.s390x
systemd-libs-257.1-1.fc42.s390x
tar-1.35-4.fc41.s390x
unzip-6.0-65.fc42.s390x
util-linux-2.40.2-8.fc42.s390x
util-linux-core-2.40.2-8.fc42.s390x
which-2.21-42.fc41.s390x
xxhash-libs-0.8.2-4.fc42.s390x
xz-5.6.3-2.fc42.s390x
xz-libs-5.6.3-2.fc42.s390x
zig-srpm-macros-1-3.fc41.noarch
zip-3.0-42.fc42.s390x
zlib-ng-compat-2.2.2-1.fc42.s390x
zstd-1.5.6-2.fc41.s390x
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1729209600
Wrote: /builddir/build/SRPMS/percolator-3.06.04-5.fc42.src.rpm
Finish: rpmbuild -bs
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-s390x-1735115967.112094/root/var/log/dnf5.log
INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz
/bin/tar: Removing leading `/' from member names
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-zsjc34sm/percolator/percolator.spec) Config(child) 0 minutes 37 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-3.06.04-5.fc42.src.rpm)  Config(fedora-rawhide-s390x)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1735115967.112094/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-s390x-bootstrap-1735115967.112094/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-1735115967.112094/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
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.20.0-1.fc42.s390x
  rpm-sequoia-1.7.0-3.fc42.s390x
  dnf5-5.2.8.1-2.fc42.s390x
  dnf5-plugins-5.2.8.1-2.fc42.s390x
Finish: chroot init
Start: build phase for percolator-3.06.04-5.fc42.src.rpm
Start: build setup for percolator-3.06.04-5.fc42.src.rpm
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1729209600
Wrote: /builddir/build/SRPMS/percolator-3.06.04-5.fc42.src.rpm
Updating and loading repositories:
 fedora                                 100% |   8.0 KiB/s |   3.8 KiB |  00m00s
 Copr repository                        100% |   4.4 KiB/s |   1.5 KiB |  00m00s
 Additional repo https_fedorapeople_org 100% |   4.7 KiB/s |   1.5 KiB |  00m00s
Repositories loaded.
Package                    Arch   Version              Repository                                                             Size
Installing:
 boost-devel               s390x  1.83.0-9.fc42        fedora                                                            143.0 MiB
 boost-static              s390x  1.83.0-9.fc42        fedora                                                             33.4 MiB
 bzip2-devel               s390x  1.0.8-19.fc42        copr_base                                                         309.8 KiB
 cmake                     s390x  3.31.3-1.fc42        fedora                                                             32.6 MiB
 gcc                       s390x  15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch  79.2 MiB
 gcc-c++                   s390x  15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch  29.9 MiB
 gtest-devel               s390x  1.14.0-5.fc42        copr_base                                                           1.0 MiB
 libtirpc-devel            s390x  1.3.6-1.fc42         fedora                                                            251.6 KiB
 make                      s390x  1:4.4.1-9.fc42       copr_base                                                           1.8 MiB
 python3-devel             s390x  3.13.1-2.fc42        fedora                                                              1.8 MiB
 sqlite-devel              s390x  3.47.2-1.fc42        fedora                                                            673.4 KiB
 tokyocabinet-devel        s390x  1.4.48-26.fc41       fedora                                                            460.2 KiB
 xerces-c-devel            s390x  3.3.0-5.fc42         fedora                                                              4.1 MiB
 xsd                       s390x  4.1.0-0.16.a11.fc42  fedora                                                              5.7 MiB
 zlib-ng-compat-devel      s390x  2.2.2-1.fc42         fedora                                                            106.8 KiB
Installing dependencies:
 annobin-docs              noarch 12.80-1.fc42         fedora                                                             98.6 KiB
 annobin-plugin-gcc        s390x  12.80-1.fc42         fedora                                                            988.6 KiB
 boost                     s390x  1.83.0-9.fc42        fedora                                                              1.3 KiB
 boost-atomic              s390x  1.83.0-9.fc42        fedora                                                             15.5 KiB
 boost-chrono              s390x  1.83.0-9.fc42        fedora                                                             31.5 KiB
 boost-container           s390x  1.83.0-9.fc42        fedora                                                             63.5 KiB
 boost-context             s390x  1.83.0-9.fc42        fedora                                                             11.3 KiB
 boost-contract            s390x  1.83.0-9.fc42        fedora                                                             95.6 KiB
 boost-coroutine           s390x  1.83.0-9.fc42        fedora                                                             19.5 KiB
 boost-date-time           s390x  1.83.0-9.fc42        fedora                                                              7.1 KiB
 boost-fiber               s390x  1.83.0-9.fc42        fedora                                                             79.6 KiB
 boost-filesystem          s390x  1.83.0-9.fc42        fedora                                                            139.8 KiB
 boost-graph               s390x  1.83.0-9.fc42        fedora                                                            356.0 KiB
 boost-iostreams           s390x  1.83.0-9.fc42        fedora                                                             87.5 KiB
 boost-json                s390x  1.83.0-9.fc42        fedora                                                            355.8 KiB
 boost-locale              s390x  1.83.0-9.fc42        fedora                                                            616.3 KiB
 boost-log                 s390x  1.83.0-9.fc42        fedora                                                              1.5 MiB
 boost-math                s390x  1.83.0-9.fc42        fedora                                                            686.0 KiB
 boost-nowide              s390x  1.83.0-9.fc42        fedora                                                             19.5 KiB
 boost-numpy3              s390x  1.83.0-9.fc42        fedora                                                             51.5 KiB
 boost-program-options     s390x  1.83.0-9.fc42        fedora                                                            275.5 KiB
 boost-python3             s390x  1.83.0-9.fc42        fedora                                                            250.9 KiB
 boost-random              s390x  1.83.0-9.fc42        fedora                                                             27.5 KiB
 boost-regex               s390x  1.83.0-9.fc42        fedora                                                            287.5 KiB
 boost-serialization       s390x  1.83.0-9.fc42        fedora                                                            449.7 KiB
 boost-stacktrace          s390x  1.83.0-9.fc42        fedora                                                             47.5 KiB
 boost-system              s390x  1.83.0-9.fc42        fedora                                                              7.1 KiB
 boost-test                s390x  1.83.0-9.fc42        fedora                                                            650.2 KiB
 boost-thread              s390x  1.83.0-9.fc42        fedora                                                            131.6 KiB
 boost-timer               s390x  1.83.0-9.fc42        fedora                                                             19.5 KiB
 boost-type_erasure        s390x  1.83.0-9.fc42        fedora                                                             51.6 KiB
 boost-wave                s390x  1.83.0-9.fc42        fedora                                                            668.2 KiB
 cmake-data                noarch 3.31.3-1.fc42        fedora                                                              8.5 MiB
 cmake-filesystem          s390x  3.31.3-1.fc42        fedora                                                              0.0   B
 cmake-rpm-macros          noarch 3.31.3-1.fc42        fedora                                                              7.5 KiB
 cpp                       s390x  15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch  26.6 MiB
 emacs-filesystem          noarch 1:30.0-3.fc41        fedora                                                              0.0   B
 expat                     s390x  2.6.4-1.fc42         copr_base                                                         299.3 KiB
 flexiblas                 s390x  3.4.4-3.fc42         copr_base                                                          48.5 KiB
 flexiblas-netlib          s390x  3.4.4-3.fc42         copr_base                                                          12.3 MiB
 flexiblas-openblas-openmp s390x  3.4.4-3.fc42         copr_base                                                          38.0 KiB
 gcc-plugin-annobin        s390x  15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch  51.3 KiB
 glibc-devel               s390x  2.40.9000-24.fc42    copr_base                                                           2.6 MiB
 gmock                     s390x  1.14.0-5.fc42        copr_base                                                         117.6 KiB
 gtest                     s390x  1.14.0-5.fc42        copr_base                                                         473.7 KiB
 jsoncpp                   s390x  1.9.5-8.fc42         copr_base                                                         244.6 KiB
 kernel-headers            s390x  6.13.0-0.rc4.36.fc42 fedora                                                              6.5 MiB
 libasan                   s390x  15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch   1.6 MiB
 libatomic                 s390x  15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch  26.0 KiB
 libb2                     s390x  0.98.1-12.fc42       copr_base                                                          40.6 KiB
 libcutl                   s390x  1.10.0-31.fc42       copr_base                                                           1.1 MiB
 libgfortran               s390x  15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch   2.4 MiB
 libicu                    s390x  76.1-1.fc42          copr_base                                                          36.6 MiB
 libicu-devel              s390x  76.1-1.fc42          copr_base                                                           5.0 MiB
 libmpc                    s390x  1.3.1-6.fc42         copr_base                                                         157.8 KiB
 libstdc++-devel           s390x  15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch  15.4 MiB
 libubsan                  s390x  15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 480.5 KiB
 libuv                     s390x  1:1.49.2-1.fc42      copr_base                                                         563.1 KiB
 libxcrypt-devel           s390x  4.4.36-12.fc42       fedora                                                             30.5 KiB
 mpdecimal                 s390x  2.5.1-16.fc42        copr_base                                                         215.7 KiB
 openblas                  s390x  0.3.28-2.fc42        copr_base                                                         106.6 KiB
 openblas-openmp           s390x  0.3.28-2.fc42        copr_base                                                          15.2 MiB
 pyproject-rpm-macros      noarch 1.16.3-1.fc42        fedora                                                            113.7 KiB
 python-pip-wheel          noarch 24.3.1-1.fc42        fedora                                                              1.2 MiB
 python-rpm-macros         noarch 3.13-3.fc41          fedora                                                             22.1 KiB
 python3                   s390x  3.13.1-2.fc42        fedora                                                             22.4 KiB
 python3-libs              s390x  3.13.1-2.fc42        fedora                                                             40.0 MiB
 python3-numpy             s390x  1:2.2.1-1.fc42       fedora                                                             36.0 MiB
 python3-numpy-f2py        s390x  1:2.2.1-1.fc42       fedora                                                              2.0 MiB
 python3-packaging         noarch 24.2-2.fc42          fedora                                                            555.7 KiB
 python3-rpm-generators    noarch 14-11.fc41           fedora                                                             81.7 KiB
 python3-rpm-macros        noarch 3.13-3.fc41          fedora                                                              6.4 KiB
 rhash                     s390x  1.4.5-1.fc42         fedora                                                            362.6 KiB
 sqlite                    s390x  3.47.2-1.fc42        fedora                                                              2.0 MiB
 tokyocabinet              s390x  1.4.48-26.fc41       fedora                                                              1.6 MiB
 tzdata                    noarch 2024b-1.fc42         fedora                                                              1.6 MiB
 vim-filesystem            noarch 2:9.1.919-1.fc42     fedora                                                             40.0   B
 xerces-c                  s390x  3.3.0-5.fc42         fedora                                                              3.7 MiB

Transaction Summary:
 Installing:        93 packages

Total size of inbound packages is 137 MiB. Need to download 137 MiB.
After this operation, 568 MiB extra will be used (install 568 MiB, remove 0 B).
[ 1/93] libtirpc-devel-0:1.3.6-1.fc42.s 100% | 211.6 KiB/s | 125.5 KiB |  00m01s
[ 2/93] sqlite-devel-0:3.47.2-1.fc42.s3 100% | 647.7 KiB/s | 150.3 KiB |  00m00s
[ 3/93] tokyocabinet-devel-0:1.4.48-26. 100% | 721.4 KiB/s |  88.7 KiB |  00m00s
[ 4/93] boost-static-0:1.83.0-9.fc42.s3 100% |   3.3 MiB/s |   3.3 MiB |  00m01s
[ 5/93] python3-devel-0:3.13.1-2.fc42.s 100% |   3.5 MiB/s | 403.0 KiB |  00m00s
[ 6/93] xerces-c-devel-0:3.3.0-5.fc42.s 100% |   2.1 MiB/s | 513.1 KiB |  00m00s
[ 7/93] xsd-0:4.1.0-0.16.a11.fc42.s390x 100% |   9.2 MiB/s |   1.3 MiB |  00m00s
[ 8/93] bzip2-devel-0:1.0.8-19.fc42.s39 100% |  11.6 MiB/s | 214.1 KiB |  00m00s
[ 9/93] zlib-ng-compat-devel-0:2.2.2-1. 100% | 328.2 KiB/s |  38.1 KiB |  00m00s
[10/93] boost-devel-0:1.83.0-9.fc42.s39 100% |   9.2 MiB/s |  14.2 MiB |  00m02s
[11/93] cmake-0:3.31.3-1.fc42.s390x     100% |  21.6 MiB/s |   9.8 MiB |  00m00s
[12/93] gtest-devel-0:1.14.0-5.fc42.s39 100% |  59.3 MiB/s | 242.7 KiB |  00m00s
[13/93] make-1:4.4.1-9.fc42.s390x       100% | 115.7 MiB/s | 592.3 KiB |  00m00s
[14/93] boost-0:1.83.0-9.fc42.s390x     100% | 113.1 KiB/s |  12.8 KiB |  00m00s
[15/93] boost-numpy3-0:1.83.0-9.fc42.s3 100% | 232.8 KiB/s |  26.3 KiB |  00m00s
[16/93] sqlite-0:3.47.2-1.fc42.s390x    100% |   7.9 MiB/s | 934.3 KiB |  00m00s
[17/93] tokyocabinet-0:1.4.48-26.fc41.s 100% |   4.1 MiB/s | 549.0 KiB |  00m00s
[18/93] xerces-c-0:3.3.0-5.fc42.s390x   100% |   8.2 MiB/s | 970.5 KiB |  00m00s
[19/93] python3-0:3.13.1-2.fc42.s390x   100% | 235.4 KiB/s |  26.6 KiB |  00m00s
[20/93] python3-libs-0:3.13.1-2.fc42.s3 100% |  19.3 MiB/s |   8.9 MiB |  00m00s
[21/93] gcc-c++-0:15.0.0-0.2.fc42.s390x 100% |   8.4 MiB/s |  11.9 MiB |  00m01s
[22/93] cmake-data-0:3.31.3-1.fc42.noar 100% |  20.9 MiB/s |   2.5 MiB |  00m00s
[23/93] cmake-filesystem-0:3.31.3-1.fc4 100% | 160.2 KiB/s |  17.6 KiB |  00m00s
[24/93] rhash-0:1.4.5-1.fc42.s390x      100% |   1.7 MiB/s | 203.1 KiB |  00m00s
[25/93] cpp-0:15.0.0-0.2.fc42.s390x     100% |  22.8 MiB/s |   9.8 MiB |  00m00s
[26/93] gmock-0:1.14.0-5.fc42.s390x     100% |  13.5 MiB/s |  55.4 KiB |  00m00s
[27/93] gtest-0:1.14.0-5.fc42.s390x     100% |  54.7 MiB/s | 167.9 KiB |  00m00s
[28/93] gcc-0:15.0.0-0.2.fc42.s390x     100% |  13.7 MiB/s |  30.8 MiB |  00m02s
[29/93] boost-atomic-0:1.83.0-9.fc42.s3 100% | 146.7 KiB/s |  16.6 KiB |  00m00s
[30/93] boost-chrono-0:1.83.0-9.fc42.s3 100% | 205.3 KiB/s |  22.6 KiB |  00m00s
[31/93] boost-container-0:1.83.0-9.fc42 100% | 338.9 KiB/s |  38.3 KiB |  00m00s
[32/93] boost-context-0:1.83.0-9.fc42.s 100% | 131.7 KiB/s |  14.5 KiB |  00m00s
[33/93] boost-contract-0:1.83.0-9.fc42. 100% | 365.7 KiB/s |  41.3 KiB |  00m00s
[34/93] boost-coroutine-0:1.83.0-9.fc42 100% | 160.3 KiB/s |  17.6 KiB |  00m00s
[35/93] boost-date-time-0:1.83.0-9.fc42 100% | 118.4 KiB/s |  13.4 KiB |  00m00s
[36/93] boost-fiber-0:1.83.0-9.fc42.s39 100% | 351.6 KiB/s |  39.0 KiB |  00m00s
[37/93] boost-filesystem-0:1.83.0-9.fc4 100% | 567.8 KiB/s |  64.2 KiB |  00m00s
[38/93] boost-graph-0:1.83.0-9.fc42.s39 100% |   1.3 MiB/s | 148.5 KiB |  00m00s
[39/93] boost-iostreams-0:1.83.0-9.fc42 100% | 322.8 KiB/s |  36.8 KiB |  00m00s
[40/93] boost-json-0:1.83.0-9.fc42.s390 100% |   1.3 MiB/s | 150.2 KiB |  00m00s
[41/93] libstdc++-devel-0:15.0.0-0.2.fc 100% |   2.4 MiB/s |   2.7 MiB |  00m01s
[42/93] boost-locale-0:1.83.0-9.fc42.s3 100% |   1.7 MiB/s | 200.5 KiB |  00m00s
[43/93] boost-nowide-0:1.83.0-9.fc42.s3 100% | 160.8 KiB/s |  18.2 KiB |  00m00s
[44/93] boost-log-0:1.83.0-9.fc42.s390x 100% |   2.0 MiB/s | 456.7 KiB |  00m00s
[45/93] boost-program-options-0:1.83.0- 100% | 895.4 KiB/s | 102.1 KiB |  00m00s
[46/93] boost-python3-0:1.83.0-9.fc42.s 100% | 797.7 KiB/s |  88.5 KiB |  00m00s
[47/93] boost-random-0:1.83.0-9.fc42.s3 100% | 184.9 KiB/s |  20.9 KiB |  00m00s
[48/93] boost-regex-0:1.83.0-9.fc42.s39 100% |   1.0 MiB/s | 116.0 KiB |  00m00s
[49/93] boost-serialization-0:1.83.0-9. 100% |   1.0 MiB/s | 122.4 KiB |  00m00s
[50/93] boost-stacktrace-0:1.83.0-9.fc4 100% | 228.2 KiB/s |  25.3 KiB |  00m00s
[51/93] boost-math-0:1.83.0-9.fc42.s390 100% | 388.0 KiB/s | 225.0 KiB |  00m01s
[52/93] boost-system-0:1.83.0-9.fc42.s3 100% | 118.6 KiB/s |  13.4 KiB |  00m00s
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[54/93] boost-thread-0:1.83.0-9.fc42.s3 100% | 488.4 KiB/s |  56.7 KiB |  00m00s
[55/93] boost-timer-0:1.83.0-9.fc42.s39 100% | 166.7 KiB/s |  18.8 KiB |  00m00s
[56/93] boost-type_erasure-0:1.83.0-9.f 100% | 269.4 KiB/s |  29.9 KiB |  00m00s
[57/93] boost-wave-0:1.83.0-9.fc42.s390 100% |   1.7 MiB/s | 207.6 KiB |  00m00s
[58/93] python-pip-wheel-0:24.3.1-1.fc4 100% |  10.3 MiB/s |   1.2 MiB |  00m00s
[59/93] tzdata-0:2024b-1.fc42.noarch    100% |   6.2 MiB/s | 712.7 KiB |  00m00s
[60/93] libmpc-0:1.3.1-6.fc42.s390x     100% |  23.1 MiB/s |  70.9 KiB |  00m00s
[61/93] glibc-devel-0:2.40.9000-24.fc42 100% | 111.0 MiB/s | 568.3 KiB |  00m00s
[62/93] emacs-filesystem-1:30.0-3.fc41. 100% |  61.6 KiB/s |   7.1 KiB |  00m00s
[63/93] vim-filesystem-2:9.1.919-1.fc42 100% | 145.4 KiB/s |  16.4 KiB |  00m00s
[64/93] libxcrypt-devel-0:4.4.36-12.fc4 100% | 239.1 KiB/s |  27.7 KiB |  00m00s
[65/93] kernel-headers-0:6.13.0-0.rc4.3 100% |   7.3 MiB/s |   1.6 MiB |  00m00s
[66/93] libatomic-0:15.0.0-0.2.fc42.s39 100% | 150.5 KiB/s |  15.8 KiB |  00m00s
[67/93] libasan-0:15.0.0-0.2.fc42.s390x 100% |   2.1 MiB/s | 478.0 KiB |  00m00s
[68/93] expat-0:2.6.4-1.fc42.s390x      100% |  27.6 MiB/s | 113.0 KiB |  00m00s
[69/93] libb2-0:0.98.1-12.fc42.s390x    100% |  25.4 MiB/s |  26.0 KiB |  00m00s
[70/93] mpdecimal-0:2.5.1-16.fc42.s390x 100% |  46.7 MiB/s |  95.7 KiB |  00m00s
[71/93] libubsan-0:15.0.0-0.2.fc42.s390 100% |   1.7 MiB/s | 198.7 KiB |  00m00s
[72/93] jsoncpp-0:1.9.5-8.fc42.s390x    100% |  30.4 MiB/s |  93.3 KiB |  00m00s
[73/93] libuv-1:1.49.2-1.fc42.s390x     100% |  63.1 MiB/s | 258.4 KiB |  00m00s
[74/93] libicu-0:76.1-1.fc42.s390x      100% | 295.7 MiB/s |  10.6 MiB |  00m00s
[75/93] python3-numpy-f2py-1:2.2.1-1.fc 100% |   4.3 MiB/s | 490.8 KiB |  00m00s
[76/93] libicu-devel-0:76.1-1.fc42.s390 100% | 146.8 MiB/s | 751.5 KiB |  00m00s
[77/93] flexiblas-netlib-0:3.4.4-3.fc42 100% | 253.3 MiB/s |   3.8 MiB |  00m00s
[78/93] flexiblas-0:3.4.4-3.fc42.s390x  100% |  12.5 MiB/s |  25.7 KiB |  00m00s
[79/93] flexiblas-openblas-openmp-0:3.4 100% |   8.1 MiB/s |  16.6 KiB |  00m00s
[80/93] openblas-openmp-0:0.3.28-2.fc42 100% | 171.0 MiB/s |   4.3 MiB |  00m00s
[81/93] libcutl-0:1.10.0-31.fc42.s390x  100% | 909.9 KiB/s | 322.1 KiB |  00m00s
[82/93] openblas-0:0.3.28-2.fc42.s390x  100% |  20.2 MiB/s |  41.4 KiB |  00m00s
[83/93] libgfortran-0:15.0.0-0.2.fc42.s 100% |   2.6 MiB/s | 588.5 KiB |  00m00s
[84/93] gcc-plugin-annobin-0:15.0.0-0.2 100% | 289.9 KiB/s |  30.4 KiB |  00m00s
[85/93] python3-numpy-1:2.2.1-1.fc42.s3 100% |  15.2 MiB/s |   7.0 MiB |  00m00s
[86/93] pyproject-rpm-macros-0:1.16.3-1 100% | 402.2 KiB/s |  44.6 KiB |  00m00s
[87/93] python-rpm-macros-0:3.13-3.fc41 100% | 152.3 KiB/s |  17.7 KiB |  00m00s
[88/93] python3-rpm-generators-0:14-11. 100% | 259.3 KiB/s |  29.3 KiB |  00m00s
[89/93] python3-rpm-macros-0:3.13-3.fc4 100% | 112.1 KiB/s |  12.4 KiB |  00m00s
[90/93] cmake-rpm-macros-0:3.31.3-1.fc4 100% | 146.4 KiB/s |  17.0 KiB |  00m00s
[91/93] python3-packaging-0:24.2-2.fc42 100% |   1.3 MiB/s | 153.8 KiB |  00m00s
[92/93] annobin-plugin-gcc-0:12.80-1.fc 100% |   8.5 MiB/s | 979.4 KiB |  00m00s
[93/93] annobin-docs-0:12.80-1.fc42.noa 100% | 271.6 KiB/s |  92.6 KiB |  00m00s
--------------------------------------------------------------------------------
[93/93] Total                           100% |  20.9 MiB/s | 137.5 MiB |  00m07s
Running transaction
[ 1/95] Verify package files            100% | 208.0   B/s |  93.0   B |  00m00s
[ 2/95] Prepare transaction             100% | 531.0   B/s |  93.0   B |  00m00s
[ 3/95] Installing boost-system-0:1.83. 100% |   7.9 MiB/s |   8.1 KiB |  00m00s
[ 4/95] Installing boost-chrono-0:1.83. 100% |   0.0   B/s |  32.5 KiB |  00m00s
[ 5/95] Installing boost-thread-0:1.83. 100% | 129.5 MiB/s | 132.6 KiB |  00m00s
[ 6/95] Installing libicu-0:76.1-1.fc42 100% | 271.3 MiB/s |  36.6 MiB |  00m00s
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[10/95] Installing expat-0:2.6.4-1.fc42 100% | 147.2 MiB/s | 301.4 KiB |  00m00s
[11/95] Installing libmpc-0:1.3.1-6.fc4 100% | 155.5 MiB/s | 159.3 KiB |  00m00s
[12/95] Installing boost-context-0:1.83 100% |   0.0   B/s |  12.3 KiB |  00m00s
[13/95] Installing boost-atomic-0:1.83. 100% |   0.0   B/s |  16.5 KiB |  00m00s
[14/95] Installing boost-filesystem-0:1 100% | 137.5 MiB/s | 140.8 KiB |  00m00s
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[16/95] Installing libgfortran-0:15.0.0 100% | 299.8 MiB/s |   2.4 MiB |  00m00s
[17/95] Installing boost-date-time-0:1. 100% |   0.0   B/s |   8.1 KiB |  00m00s
[18/95] Installing boost-container-0:1. 100% |   0.0   B/s |  64.5 KiB |  00m00s
[19/95] Installing gtest-0:1.14.0-5.fc4 100% | 154.6 MiB/s | 475.1 KiB |  00m00s
[20/95] Installing xerces-c-0:3.3.0-5.f 100% | 309.2 MiB/s |   3.7 MiB |  00m00s
[21/95] Installing make-1:4.4.1-9.fc42. 100% | 264.8 MiB/s |   1.9 MiB |  00m00s
[22/95] Installing gmock-0:1.14.0-5.fc4 100% | 116.3 MiB/s | 119.1 KiB |  00m00s
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[25/95] Installing pyproject-rpm-macros 100% | 113.0 MiB/s | 115.7 KiB |  00m00s
[26/95] Installing boost-fiber-0:1.83.0 100% |  78.7 MiB/s |  80.6 KiB |  00m00s
[27/95] Installing boost-log-0:1.83.0-9 100% | 249.5 MiB/s |   1.5 MiB |  00m00s
[28/95] Installing boost-coroutine-0:1. 100% |   0.0   B/s |  20.6 KiB |  00m00s
[29/95] Installing cpp-0:15.0.0-0.2.fc4 100% | 266.4 MiB/s |  26.6 MiB |  00m00s
[30/95] Installing libcutl-0:1.10.0-31. 100% | 267.5 MiB/s |   1.1 MiB |  00m00s
[31/95] Installing boost-graph-0:1.83.0 100% | 174.3 MiB/s | 357.0 KiB |  00m00s
[32/95] Installing boost-locale-0:1.83. 100% | 200.9 MiB/s | 617.3 KiB |  00m00s
[33/95] Installing libicu-devel-0:76.1- 100% | 298.3 MiB/s |   5.1 MiB |  00m00s
[34/95] Installing boost-type_erasure-0 100% |   0.0   B/s |  52.6 KiB |  00m00s
[35/95] Installing boost-timer-0:1.83.0 100% |   0.0   B/s |  20.5 KiB |  00m00s
[36/95] Installing annobin-docs-0:12.80 100% |   0.0   B/s |  99.7 KiB |  00m00s
[37/95] Installing openblas-0:0.3.28-2. 100% |   0.0   B/s | 108.3 KiB |  00m00s
[38/95] Installing openblas-openmp-0:0. 100% | 286.2 MiB/s |  15.2 MiB |  00m00s
[39/95] Installing flexiblas-0:3.4.4-3. 100% |   0.0   B/s |  49.7 KiB |  00m00s
[40/95] Installing flexiblas-openblas-o 100% |   0.0   B/s |  38.9 KiB |  00m00s
[41/95] Installing flexiblas-netlib-0:3 100% | 279.3 MiB/s |  12.3 MiB |  00m00s
[42/95] Installing libuv-1:1.49.2-1.fc4 100% | 276.3 MiB/s | 565.9 KiB |  00m00s
[43/95] Installing jsoncpp-0:1.9.5-8.fc 100% | 240.4 MiB/s | 246.1 KiB |  00m00s
[44/95] Installing mpdecimal-0:2.5.1-16 100% | 211.8 MiB/s | 216.8 KiB |  00m00s
[45/95] Installing libb2-0:0.98.1-12.fc 100% |   0.0   B/s |  41.7 KiB |  00m00s
[46/95] Installing libubsan-0:15.0.0-0. 100% | 235.0 MiB/s | 481.4 KiB |  00m00s
[47/95] Installing libatomic-0:15.0.0-0 100% |   0.0   B/s |  26.9 KiB |  00m00s
[48/95] Installing libasan-0:15.0.0-0.2 100% | 198.9 MiB/s |   1.6 MiB |  00m00s
[49/95] Installing kernel-headers-0:6.1 100% | 179.1 MiB/s |   6.6 MiB |  00m00s
[50/95] Installing libxcrypt-devel-0:4. 100% |  16.0 MiB/s |  32.9 KiB |  00m00s
[51/95] Installing glibc-devel-0:2.40.9 100% | 165.1 MiB/s |   2.6 MiB |  00m00s
[52/95] Installing gcc-0:15.0.0-0.2.fc4 100% | 278.0 MiB/s |  79.2 MiB |  00m00s
[53/95] Installing vim-filesystem-2:9.1 100% |   4.6 MiB/s |   4.7 KiB |  00m00s
[54/95] Installing emacs-filesystem-1:3 100% | 106.2 KiB/s | 544.0   B |  00m00s
[55/95] Installing tzdata-0:2024b-1.fc4 100% |  53.8 MiB/s |   1.9 MiB |  00m00s
[56/95] Installing python-pip-wheel-0:2 100% | 155.5 MiB/s |   1.2 MiB |  00m00s
[57/95] Installing python3-libs-0:3.13. 100% | 259.0 MiB/s |  40.4 MiB |  00m00s
[58/95] Installing python3-0:3.13.1-2.f 100% |   0.0   B/s |  24.2 KiB |  00m00s
[59/95] Installing boost-python3-0:1.83 100% | 246.0 MiB/s | 251.9 KiB |  00m00s
[60/95] Installing cmake-rpm-macros-0:3 100% |   0.0   B/s |   8.2 KiB |  00m00s
[61/95] Installing python3-packaging-0: 100% | 184.9 MiB/s | 568.0 KiB |  00m00s
[62/95] Installing python3-rpm-generato 100% |  81.0 MiB/s |  82.9 KiB |  00m00s
[63/95] Installing python3-devel-0:3.13 100% | 129.7 MiB/s |   1.8 MiB |  00m00s
[64/95] Installing python3-numpy-1:2.2. 100% | 293.0 MiB/s |  36.3 MiB |  00m00s
[65/95] Installing python3-numpy-f2py-1 100% | 159.0 MiB/s |   2.1 MiB |  00m00s
[66/95] Installing boost-numpy3-0:1.83. 100% |   0.0   B/s |  52.5 KiB |  00m00s
[67/95] Installing boost-test-0:1.83.0- 100% | 212.1 MiB/s | 651.5 KiB |  00m00s
[68/95] Installing boost-stacktrace-0:1 100% |  48.2 MiB/s |  49.4 KiB |  00m00s
[69/95] Installing boost-serialization- 100% | 220.3 MiB/s | 451.2 KiB |  00m00s
[70/95] Installing boost-random-0:1.83. 100% |   0.0   B/s |  28.5 KiB |  00m00s
[71/95] Installing boost-program-option 100% | 135.0 MiB/s | 276.6 KiB |  00m00s
[72/95] Installing boost-nowide-0:1.83. 100% |   0.0   B/s |  20.5 KiB |  00m00s
[73/95] Installing boost-math-0:1.83.0- 100% | 224.4 MiB/s | 689.3 KiB |  00m00s
[74/95] Installing boost-iostreams-0:1. 100% |  86.4 MiB/s |  88.5 KiB |  00m00s
[75/95] Installing boost-contract-0:1.8 100% |  94.3 MiB/s |  96.6 KiB |  00m00s
[76/95] Installing boost-0:1.83.0-9.fc4 100% |  40.9 KiB/s |   1.7 KiB |  00m00s
[77/95] Installing boost-devel-0:1.83.0 100% | 231.0 MiB/s | 145.8 MiB |  00m01s
[78/95] Installing libstdc++-devel-0:15 100% | 305.4 MiB/s |  15.6 MiB |  00m00s
[79/95] Installing rhash-0:1.4.5-1.fc42 100% |  29.9 MiB/s | 367.9 KiB |  00m00s
[80/95] Installing cmake-data-0:3.31.3- 100% |  99.5 MiB/s |   9.1 MiB |  00m00s
[81/95] Installing cmake-0:3.31.3-1.fc4 100% | 299.1 MiB/s |  32.6 MiB |  00m00s
[82/95] Installing tokyocabinet-0:1.4.4 100% | 198.8 MiB/s |   1.6 MiB |  00m00s
[83/95] Installing sqlite-0:3.47.2-1.fc 100% | 247.6 MiB/s |   2.0 MiB |  00m00s
[84/95] Installing sqlite-devel-0:3.47. 100% | 329.2 MiB/s | 674.1 KiB |  00m00s
[85/95] Installing tokyocabinet-devel-0 100% | 226.2 MiB/s | 463.3 KiB |  00m00s
[86/95] Installing gcc-c++-0:15.0.0-0.2 100% | 271.6 MiB/s |  29.9 MiB |  00m00s
[87/95] Installing boost-static-0:1.83. 100% | 445.3 MiB/s |  33.4 MiB |  00m00s
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[89/95] Installing annobin-plugin-gcc-0 100% |  74.4 MiB/s | 990.2 KiB |  00m00s
[90/95] Installing xsd-0:4.1.0-0.16.a11 100% | 238.8 MiB/s |   5.7 MiB |  00m00s
[91/95] Installing gtest-devel-0:1.14.0 100% | 150.2 MiB/s |   1.1 MiB |  00m00s
[92/95] Installing xerces-c-devel-0:3.3 100% | 233.9 MiB/s |   4.2 MiB |  00m00s
[93/95] Installing zlib-ng-compat-devel 100% | 105.8 MiB/s | 108.3 KiB |  00m00s
[94/95] Installing bzip2-devel-0:1.0.8- 100% | 303.5 MiB/s | 310.7 KiB |  00m00s
[95/95] Installing libtirpc-devel-0:1.3 100% |   1.9 MiB/s | 263.1 KiB |  00m00s
Warning: skipped OpenPGP checks for 29 packages from repositories: copr_base, https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch
Complete!
Finish: build setup for percolator-3.06.04-5.fc42.src.rpm
Start: rpmbuild percolator-3.06.04-5.fc42.src.rpm
Building target platforms: s390x
Building for target s390x
setting SOURCE_DATE_EPOCH=1729209600
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.m1xBcv
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.06.04-build
+ test -d /builddir/build/BUILD/percolator-3.06.04-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/percolator-3.06.04-build
+ /usr/bin/rm -rf /builddir/build/BUILD/percolator-3.06.04-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-3.06.04-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-3.06.04-build/SPECPARTS
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.wKuCUw
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.06.04-build
+ cd /builddir/build/BUILD/percolator-3.06.04-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
+ /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.4ubhcw
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.06.04-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -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=-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/percolator ~/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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=-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 15.0.0
-- The CXX compiler identification is GNU 15.0.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- CMAKE_PREFIX_PATH = ../
-- XML_SUPPORT = ON
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = s390x
-- TOOL CHAIN FILE = 
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages:
-- Found Xerces-C: /usr/lib64/libxerces-c.so
--               : /usr/include
--        Version: 3.3.0
-- 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 (1.1s)
-- 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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04 -B/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/CMakeFiles /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
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make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/Globals.cpp
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[  3%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/Logger.cpp
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cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/MyException.cpp
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cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/picked_protein/Peptide.cpp
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/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/picked_protein/Peptide.cpp: In member function ‘PercolatorCrux::Peptide::getProteinIds()’:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/picked_protein/Peptide.cpp:985:12: warning: ‘__strncpy_chk’ specified bound depends on the length of the source argument [-Wstringop-truncation]
  985 |     strncpy(protein_field_tail, protein_id, protein_field_free);
      |            ^
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/picked_protein/Peptide.cpp:976:35: note: length computed here
  976 |     size_t protein_id_len = strlen(protein_id);
      |                             ~~~~~~^~~~~~~~~~~~
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cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/picked_protein/Protein.cpp: In member function ‘PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)’:
/builddir/build/BUILD/percolator-3.06.04-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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/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/parser.cxx: In constructor ‘parser_impl::parser_impl()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/parser.cxx:102:22: warning:   ‘xercesc_3_3::DOMImplementation& parser_impl::dom_impl_’ [-Wreorder]
  102 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/parser.cxx: In member function ‘xsd::cxx::xml::dom::auto_ptr<xercesc_3_3::DOMDocument> parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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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[ 12%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/percolator/src/percolator_out.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 26%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:4:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/StringTable.h:9,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.h:6:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.h:8:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘void BasicBigraph::clonePSM(int)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘BasicBigraph BasicBigraph::buildSubgraph(const Set&, const Set&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘int BasicBigraph::markSectionPartitions()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.h:9:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56:   required from here
  381 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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]’
   44 |       if ( iter->data == data )
      |            ~~~~~~~~~~~^~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8:   required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
   18 |   if ( searchList( table[index], data ) != -1 )
      |        ^~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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]’
   10 |     if ( ht.add(rhs[k]) ) {
      |          ~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56:   required from here
  381 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 27%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.cpp:24:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 30%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/MassHandler.cpp
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[ 31%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/PSMDescription.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PSMDescription.cpp:21:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PSMDescription.h: In constructor ‘PSMDescription::PSMDescription()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/PSMDescription.h:122:7: warning:   ‘int PSMDescription::specFileNr’ [-Wreorder]
  122 |   int specFileNr;
      |       ^~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PSMDescription.cpp:23:1: warning:   when initialized here [-Wreorder]
   23 | PSMDescription::PSMDescription() :
      | ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PSMDescription.h: In constructor ‘PSMDescription::PSMDescription(const std::string&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/PSMDescription.h:122:7: warning:   ‘int PSMDescription::specFileNr’ [-Wreorder]
  122 |   int specFileNr;
      |       ^~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 32%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/ResultHolder.cpp
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make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 29%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:4:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘void BasicGroupBigraph::groupProteinsBy(const Array<Set>&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberAssociatedProteins(int) const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityE(const Model&) const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::logNumberOfConfigurations() const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityRGivenN(const Array<Counter>&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityEOverAllAlphaBeta(const GridModel&) const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56:   required from here
   71 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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]’
   44 |       if ( iter->data == data )
      |            ~~~~~~~~~~~^~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8:   required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
   18 |   if ( searchList( table[index], data ) != -1 )
      |        ^~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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]’
   10 |     if ( ht.add(rhs[k]) ) {
      |          ~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56:   required from here
   71 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 33%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/XMLInterface.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/XMLInterface.h:30,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/XMLInterface.h:111:8: warning:   ‘bool XMLInterface::printDecoys_’ [-Wreorder]
  111 |   bool printDecoys_, printExpMass_;
      |        ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/XMLInterface.cpp: In member function ‘void XMLInterface::writePepXML_PSMs(Scores&, double, std::string)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/SetHandler.cpp:18:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 37%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/StdvNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 34%] Building CXX object src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:4:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<double> GroupPowerBigraph::proteinProbs()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getGroupProtNames()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::printProteinWeights() const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/srcmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
/fido/GroupPowerBigraph.cpp: In member function ‘double GroupPowerBigraph::getLogNumberStates() const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<BasicBigraph> GroupPowerBigraph::iterativePartitionSubgraphs(BasicBigraph&, double)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::initialize(BasicBigraph&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 39%] Building CXX object src/fido/CMakeFiles/fido.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 38%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/svm.cpp
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/svm.cpp: In function ‘svm_train_one(svm_problem const*, svm_parameter const*, double, double)’:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/svm.cpp:1577:14: warning: ‘si.rho’ may be used uninitialized [-Wmaybe-uninitialized]
 1577 |   f.rho = si.rho;
      |           ~~~^~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/svm.cpp:1538:24: note: ‘si’ declared here
 1538 |   Solver::SolutionInfo si;
      |                        ^~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/svm.cpp: In function ‘svm_train’:
/builddir/build/BUILD/percolator-3.06.04-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++/15/bits/std_abs.h:44,
                 from /usr/include/c++/15/cmath:59,
                 from /usr/include/c++/15/math.h:36,
                 from /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 40%] Building CXX object src/fido/CMakeFiles/fido.dir/Random.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Random.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 43%] Building CXX object src/fido/CMakeFiles/fido.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.cpp:4:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 44%] Building CXX object src/fido/CMakeFiles/fido.dir/Vector.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.cpp:4:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp:59:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
   59 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:14:8: note:   by ‘void Set::add(int)’
   14 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 45%] Linking CXX static library libfido.a
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 45%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/CrossValidation.h:28,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/CrossValidation.cpp:18:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/CrossValidation.h:29:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::preIterationSetup(Scores&, SanityCheck*, Normalizer*, FeatureMemoryPool&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(Normalizer*, double)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
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[ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/Enzyme.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/Globals.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 41%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/Caller.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Caller.h:36,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Caller.h: In constructor ‘Caller::Caller()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Caller.h:97:8: warning:   ‘bool Caller::xmlPrintDecoys_’ [-Wreorder]
   97 |   bool xmlPrintDecoys_, xmlPrintExpMass_;
      |        ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Caller.cpp:36:1: warning:   when initialized here [-Wreorder]
   36 | Caller::Caller() :
      | ^~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Caller.cpp:36:1: warning:   when initialized here [-Wreorder]
   36 | Caller::Caller() :
      | ^~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/Normalizer.cpp
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[ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/NoNormalizer.cpp
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/NoNormalizer.cpp:49:10: warning: unused variable ‘sum’ [-Wunused-variable]
   49 |   double sum = 0;
      |          ^~~
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make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/UniNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/SanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/FeatureNames.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.cpp:27:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 54%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/DataSet.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.cpp:18:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 58%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:238:10: warning:   ‘double ProteinProbEstimator::pi0_’ [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:237:8: warning:   ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder]
  237 |   bool usePi0_;
      |        ^~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:240:10: warning:   ‘double ProteinProbEstimator::fdr_’ [-Wreorder]
  240 |   double fdr_;
      |          ^~~~
/builddir/build/BUILD/percolator-3.06.04-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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.cpp:37:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp:59:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
   59 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:14:8: note:   by ‘void Set::add(int)’
   14 |   void add(int el);
      |        ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/ProteinFDRestimator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/PseudoRandom.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/SqtSanityCheck.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/ssl.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.cpp:8:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp:59:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
   59 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:14:8: note:   by ‘void Set::add(int)’
   14 |   void add(int el);
      |        ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/PackedMatrix.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedMatrix.h:11,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedMatrix.cpp:8:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp:59:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
   59 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:14:8: note:   by ‘void Set::add(int)’
   14 |   void add(int el);
      |        ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/Matrix.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/Matrix.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Matrix.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Matrix.cpp:4:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp:59:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
   59 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:14:8: note:   by ‘void Set::add(int)’
   14 |   void add(int el);
      |        ^~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Matrix.cpp: In member function ‘const Matrix& Matrix::operator=(const Array<Array<double> >&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Matrix.cpp: In function ‘Array<Array<double> > operator-(const Array<Array<double> >&)’:
/builddir/build/BUILD/percolator-3.06.04-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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 70%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/Logger.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/MyException.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/FidoInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/FidoInterface.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/FidoInterface.h:20,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/FidoInterface.cpp:18:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/FidoInterface.h:106:8: warning:   ‘bool FidoInterface::doGridSearch_’ [-Wreorder]
  106 |   bool doGridSearch_;
      |        ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/FidoInterface.cpp: In member function ‘double FidoInterface::estimatePriors(Scores&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 74%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/ProteinScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinScoreHolder.h: In constructor ‘ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/ProteinScoreHolder.h:106:7: warning:   ‘int ProteinScoreHolder::groupId_’ [-Wreorder]
  106 |   int groupId_;
      |       ^~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 62%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.cpp:35:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.cpp:167:10: warning: unused variable ‘RT’ [-Wunused-variable]
  167 |   double RT = pPSM->getRetentionTime();
      |          ^~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/FeatureMemoryPool.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/PickedProteinInterface.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PickedProteinInterface.h:27,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp:59:6: warning: ‘void Array<T>::add(const T&) [with T = int]’ was hidden [-Woverloaded-virtual=]
   59 | void Array<T>::add(const T & element)
      |      ^~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:14:8: note:   by ‘void Set::add(int)’
   14 |   void add(int el);
      |        ^~~
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/PickedProteinInterface.h:85:8: warning:   ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |        ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/PickedProteinInterface.h:83:26: warning:   ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder]
   83 |   ProteinInferenceMethod protInferenceMethod_;
      |                          ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*)’:
/builddir/build/BUILD/percolator-3.06.04-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()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
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[ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/TmpDir.cpp
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[ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/ValidateTabFile.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ValidateTabFile.h:6,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ValidateTabFile.cpp:1:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
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/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
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[ 84%] Built target perclibrary
make[1]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend
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cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color="
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/usr/bin/make  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/qvality /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/qvality /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake "--color="
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make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/qvality/qvality_main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/./PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/./BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/./LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/./PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/qvality/qvality_main.cpp:20:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 86%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Caller.h:36,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/main.cpp:18:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 88%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wl,--dependency-file=CMakeFiles/qvality.dir/link.d CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality   -L/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src  ../libperclibrary.a ../fido/libfido.a
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/usr/bin/make  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/depend
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cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/Unit_tests_Percolator_main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 91%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Fido.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Fido.cpp:24:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 94%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp:23:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:20:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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)
      |        ^
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp: In member function ‘virtual void SetHandlerTest_TestGetOptionalFields_Test::TestBody()’:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:100:17: warning: ignoring return value of ‘bool std::vector<_Tp, _Alloc>::empty() const [with _Tp = OptionalField; _Alloc = std::allocator<OptionalField>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
  100 |     fields.empty();
      |     ~~~~~~~~~~~~^~
In file included from /usr/include/c++/15/vector:68,
                 from /usr/include/gtest/gtest.h:62,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:18:
/usr/include/c++/15/bits/stl_vector.h:1222:7: note: declared here
 1222 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:102:17: warning: ignoring return value of ‘bool std::vector<_Tp, _Alloc>::empty() const [with _Tp = OptionalField; _Alloc = std::allocator<OptionalField>]’, declared with attribute ‘nodiscard’ [-Wunused-result]
  102 |     fields.empty();
      |     ~~~~~~~~~~~~^~
/usr/include/c++/15/bits/stl_vector.h:1222:7: note: declared here
 1222 |       empty() const _GLIBCXX_NOEXCEPT
      |       ^~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp:23:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp:24:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:19:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 89%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wl,--dependency-file=CMakeFiles/percolator.dir/link.d 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-3.06.04-build/percolator-rel-3-06-04/percolator'
In function ‘readRawSequence’,
    inlined from ‘parseProteinFastaFile’ at /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/picked_protein/Protein.cpp: In member function ‘parseProteinFastaFile’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
[100%] Built target percolator
make[1]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[100%] Linking CXX executable gtest_unit
cd /builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wl,--dependency-file=CMakeFiles/gtest_unit.dir/link.d 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-3.06.04-build/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[100%] Built target gtest_unit
make[1]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/CMakeFiles 0
+ popd
~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04
+ mkdir -p fido
+ pushd fido
~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido ~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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=-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 15.0.0
-- The CXX compiler identification is GNU 15.0.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done (0.4s)
-- 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-3.06.04-build/percolator-rel-3-06-04/fido
+ /usr/bin/make -O -j2 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido -B/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/fido/CMakeFiles /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/fido'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido/CMakeFiles/fido.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.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++/15/string:51,
                 from /usr/include/c++/15/bits/locale_classes.h:42,
                 from /usr/include/c++/15/bits/ios_base.h:43,
                 from /usr/include/c++/15/ios:46,
                 from /usr/include/c++/15/ostream:42,
                 from /usr/include/c++/15/iostream:43,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:11,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7:
/usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/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++/15/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++/15/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘void BasicGroupBigraph::groupProteinsBy(const Array<Set>&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberAssociatedProteins(int) const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityE(const Model&) const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido'
-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::logNumberOfConfigurations() const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityRGivenN(const Array<Counter>&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityEOverAllAlphaBeta(const GridModel&) const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56:   required from here
   71 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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++) {
      |                   ~~^~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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]’
   44 |       if ( iter->data == data )
      |            ~~~~~~~~~~~^~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8:   required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
   18 |   if ( searchList( table[index], data ) != -1 )
      |        ^~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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]’
   10 |     if ( ht.add(rhs[k]) ) {
      |          ~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56:   required from here
   71 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-3.06.04-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++/15/string:51,
                 from /usr/include/c++/15/bits/locale_classes.h:42,
                 from /usr/include/c++/15/bits/ios_base.h:43,
                 from /usr/include/c++/15/ios:46,
                 from /usr/include/c++/15/istream:42,
                 from /usr/include/c++/15/fstream:42,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.h:4:
/usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/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++/15/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++/15/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘void BasicBigraph::clonePSM(int)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘BasicBigraph BasicBigraph::buildSubgraph(const Set&, const Set&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘int BasicBigraph::markSectionPartitions()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.h:9:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56:   required from here
  381 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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++) {
      |                   ~~^~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/StringTable.h:9,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.h:6:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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]’
   44 |       if ( iter->data == data )
      |            ~~~~~~~~~~~^~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8:   required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
   18 |   if ( searchList( table[index], data ) != -1 )
      |        ^~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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]’
   10 |     if ( ht.add(rhs[k]) ) {
      |          ~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56:   required from here
  381 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Random.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido'
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido'
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.cpp
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.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++/15/string:51,
                 from /usr/include/c++/15/bits/locale_classes.h:42,
                 from /usr/include/c++/15/bits/ios_base.h:43,
                 from /usr/include/c++/15/ios:46,
                 from /usr/include/c++/15/ostream:42,
                 from /usr/include/c++/15/iostream:43,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/Array.h:11,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7:
/usr/include/c++/15/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++/15/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++/15/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++/15/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++/15/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++/15/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++/15/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<double> GroupPowerBigraph::proteinProbs()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getGroupProtNames()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::printProteinWeights() const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:77:21: warning: comparison of integer expressions of different signedness: ‘int’ and âmake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido'
€˜size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   77 |   for (int k = 0; k < groupProtNames_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘double GroupPowerBigraph::getLogNumberStates() const’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<BasicBigraph> GroupPowerBigraph::iterativePartitionSubgraphs(BasicBigraph&, double)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::initialize(BasicBigraph&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/fido'
make[1]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido'
[100%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido/CMakeFiles 0
+ popd
~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04
+ mkdir -p converters
+ pushd converters
~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters ~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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=-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 15.0.0
-- The CXX compiler identification is GNU 15.0.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR-CONVERTERS:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- Indicate the type of XML serialization scheme :
		  -DSERIALIZE="Boost" or -DSERIALIZE="TokyoCabinet"
		  or -DSERIALIZE="LevelDB".
		  By setting up the variable SERIALIZE to either Boost
		  or TokyoCabinet or LevelDB you will choose the serialization
		  scheme that will be used to build Converters.
		  Boost serialization option will be used as default if no option is given.
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- XML_SUPPORT = ON
-- PERCOLATOR_SOURCE_DIR = /builddir/build/BUILD/percolator-3.06.04-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: 3.3.0
-- 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-3.06.04-build/percolator-rel-3-06-04/converters/gaml_tandem1.0.cxx;/builddir/build/BUILD/percolator-3.06.04-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 "1.3.1")
-- ZLIB found: /usr/include, /usr/lib64/libz.so
-- Using FragSpectrumScanDatabaseTokyodb.cpp
-- Configuring done (1.1s)
-- 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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters -B/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters/CMakeFiles /builddir/build/BUILD/percolator-3.06.04-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
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cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake "--color="
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cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake "--color="
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/usr/bin/make  -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/build
make[1]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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make[1]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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[  7%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp_base64.cpp
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cd /builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp
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/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function ‘RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.h:134,
                 from /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function ‘rampSelfTest(char*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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/usr/bin/ar qc libRAMP.a CMakeFiles/RAMP.dir/ramp_base64.cpp.o CMakeFiles/RAMP.dir/ramp.cpp.o
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/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/parser.cxx: In constructor ‘parser_impl::parser_impl()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/parser.cxx:102:22: warning:   ‘xercesc_3_3::DOMImplementation& parser_impl::dom_impl_’ [-Wreorder]
  102 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/parser.cxx: In member function ‘xsd::cxx::xml::dom::auto_ptr<xercesc_3_3::DOMDocument> parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.H:28,
                 from /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In function ‘LazyMatrix* flip_lazy_matrix(LazyMatrix&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In copy constructor ‘LazyMatrix::LazyMatrix(const self&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_cols(int, int)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_start_cols(int)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_stop_cols(int)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::column_shift(int)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::linear_shift(int)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:409:31: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  409 |     for ( uint i = offset ; i < nrows - static_cast<int>(offset); i++ ) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-3.06.04-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++ ) {
      |                                                                          ~~^~~~~~~
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[ 44%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSObject.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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[ 46%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.h:4,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.h:4,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::appendFile(Spectrum&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::appendFile(char*, MSObject&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘bool MSReader::executeSqlStmt(Spectrum&, char*)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::writeCompressSpec(FILE*, Spectrum&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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:970,
                 from /usr/include/c++/15/cstdio:47,
                 from /usr/include/c++/15/parallel/compiletime_settings.h:33,
                 from /usr/include/c++/15/parallel/parallel.h:37,
                 from /usr/include/c++/15/parallel/base.h:40,
                 from /usr/include/c++/15/parallel/algobase.h:40,
                 from /usr/include/c++/15/bits/stl_algobase.h:2311,
                 from /usr/include/c++/15/vector:64,
                 from /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘MSReader::appendFile(Spectrum&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
[ 48%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSSingleScan.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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[ 50%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSTAllRT.cpp
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSTAllRT.cpp: In function ‘int main(int, char**)’:
/builddir/build/BUILD/percolator-3.06.04-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;
      |                      ^~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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[ 51%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSTDemo.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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[ 53%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSWarper.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSWarper.cpp:17:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48:
/builddir/build/BUILD/percolator-3.06.04-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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cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.cpp
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.cpp: In member function ‘bool Spectrum::getRawFilter(char*, int)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/Reader.cpp
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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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/SqtReader.cpp
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make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘void crawutils::rankties(std::vector<float>&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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++)
      |                           ~~^~~~~~~~
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[ 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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MzidentmlReader.cpp
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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) {
      |                           ^
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[ 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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/SequestReader.cpp
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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);
      |              ^~~~~~~~~~~~~~
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[ 64%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48,
                 from /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::init_transitions_from_labels()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::tabular_input(std::ifstream&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::calc_bp_chrom()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::time_interpolate(double, msmat&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::get_median() const’:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1266:make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::get_avg(int) const’:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In function ‘msmat* test_msmat(int, char**)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
[ 69%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24,
                 from /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.H:20,
                 from /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:20:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp: In member function ‘msmat_header_parser::load_strmap_from_str(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, float, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
[ 73%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24,
                 from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48,
                 from /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp: In function ‘int main(int, char**)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
[ 75%] Linking CXX static library libMSToolkit.a
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/cmake -P CMakeFiles/MSToolkit.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.06.04-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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make[1]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
[ 75%] Built target MSToolkit
make[1]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
[ 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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabase.cpp
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabase.cpp: In member function ‘std::string FragSpectrumScanDatabase::decoratePeptide(const percolatorInNs::peptideType&)’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/TandemReader.cpp
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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);
      |                      ~~~~~~~^~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp: In member function ‘virtual void FragSpectrumScanDatabaseTokyoDB::putFSS(percolatorInNs::fragSpectrumScan&)’:
/builddir/build/BUILD/percolator-3.06.04-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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make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
In file included from /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/Interface.cpp:18:
/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/Interface.h: In constructor ‘Interface::Interface()’:
/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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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In function ‘strchr’,
    inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
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  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-3.06.04-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
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make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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-3.06.04-build/percolator-rel-3-06-04/src/converters/Tandem2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wl,--dependency-file=CMakeFiles/msgf2pin.dir/link.d CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -o msgf2pin   -L/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
In function ‘strchr’,
    inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
[100%] Built target msgf2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-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 -Wl,--dependency-file=CMakeFiles/tandem2pin.dir/link.d CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -o tandem2pin   -L/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
In function ‘strchr’,
    inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/CMakeFiles 0
+ popd
~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Gl08gm
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.06.04-build
+ '[' /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT
++ dirname /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/percolator-3.06.04-build
+ mkdir /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -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=-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/BUILD/percolator-3.06.04-build/BUILDROOT 'INSTALL=/usr/bin/install -p' -C percolator
make: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04 -B/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator/CMakeFiles /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/picked_protein /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/picked_protein /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/blas /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/blas /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/blas/CMakeFiles/blas.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/fido /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/qvality /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/qvality /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/tests/unit_tests/percolator /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/percolator'
[100%] Built target gtest_unit
make[1]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Installing: /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/bin/percolator
-- Installing: /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/bin/qvality
-- Installing: /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/./bin/gtest_unit
make: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT 'INSTALL=/usr/bin/install -p' -C converters
make: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters -B/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters/CMakeFiles /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/CMakeFiles/converters.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-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-3.06.04-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-3.06.04-build/percolator-rel-3-06-04/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/bin/msgf2pin
-- Installing: /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/bin/sqt2pin
-- Installing: /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/bin/tandem2pin
-- Installing: /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/percolator/xml-1-1/mzIdentML1.1.0.xsd
-- Installing: /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/percolator/xml-2011.12.01.1/gaml_tandem1.0.xsd
-- Installing: /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/percolator/xml-2011.12.01.1/tandem2011.12.01.1.xsd
make: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
+ mkdir -p /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator
++ find . -type f '(' -name '*.a' ')'
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/blas/libblas.a /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/fido/libfido.a /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/picked_protein/libpicked_protein.a /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./fido/libfido.a /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/RAMP/libRAMP.a /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/libMSToolkit.a /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libperclibrary_part.a /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libconverters.a /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator
+ rm -f /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/bin/gtest_unit
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 3.06.04-5.fc42 --unique-debug-suffix -3.06.04-5.fc42.s390x --unique-debug-src-base percolator-3.06.04-5.fc42.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-5.fc42.s390x
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
+ /usr/bin/add-determinism --brp -j2 /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT
/builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator/libblas.a: replacing with normalized version
/builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator/libpicked_protein.a: replacing with normalized version
/builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator/libfido.a: replacing with normalized version
/builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator/libRAMP.a: replacing with normalized version
/builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator/libMSToolkit.a: replacing with normalized version
/builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator/libperclibrary.a: replacing with normalized version
/builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator/libperclibrary_part.a: replacing with normalized version
/builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/lib64/percolator/libconverters.a: replacing with normalized version
Scanned 38 directories and 196 files,
               processed 8 inodes,
               8 modified (8 replaced + 0 rewritten),
               0 unsupported format, 0 errors
Reading /builddir/build/BUILD/percolator-3.06.04-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.9rzTdl
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.06.04-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -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=-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
~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/test ~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04
+ pushd test
+ ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt

Pin-converter version 3.06.4, Build Date Oct 18 2024 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 025b65b888c843f18ac898119667090f
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 Oct 18 2024 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 Wed Dec 25 08:46:32 2024
 on 025b65b888c843f18ac898119667090f
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 0.5640 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 20.9286 cpu seconds or 13 seconds wall clock time.
~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04
~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator ~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04
+ popd
+ pushd percolator
+ /usr/bin/ctest --test-dir . --output-on-failure --force-new-ctest-process -j2
Test project /builddir/build/BUILD/percolator-3.06.04-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-3.06.04-build/percolator-rel-3-06-04
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: percolator-3.06.04-5.fc42.s390x
Provides: percolator = 3.06.04-5.fc42 percolator(s390-64) = 3.06.04-5.fc42
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_1.3.15)(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-3.3.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-3.06.04-5.fc42.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.athqWT
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.06.04-build
+ cd percolator-rel-3-06-04
+ DOCDIR=/builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/doc/percolator-data
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/ReadMe.txt /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-README /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/doc/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.yH1jzP
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.06.04-build
+ cd percolator-rel-3-06-04
+ LICENSEDIR=/builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/licenses/percolator-data
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/licenses/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/license.txt /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/licenses/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/RAMP_license_lgpl-2.1.txt /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/licenses/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-data = 3.06.04-5.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-static-3.06.04-5.fc42.s390x
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.3U8dKQ
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.06.04-build
+ cd percolator-rel-3-06-04
+ DOCDIR=/builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/doc/percolator-static
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/ReadMe.txt /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-README /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/doc/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.o9lPzz
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.06.04-build
+ cd percolator-rel-3-06-04
+ LICENSEDIR=/builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/licenses/percolator-static
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/licenses/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/license.txt /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/licenses/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/RAMP_license_lgpl-2.1.txt /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT/usr/share/licenses/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-static = 3.06.04-5.fc42 percolator-static(s390-64) = 3.06.04-5.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debugsource-3.06.04-5.fc42.s390x
Provides: percolator-debugsource = 3.06.04-5.fc42 percolator-debugsource(s390-64) = 3.06.04-5.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debuginfo-3.06.04-5.fc42.s390x
Provides: debuginfo(build-id) = 41516b83472dffcdb69124a81873699241c60b0e debuginfo(build-id) = 6bd2d85521678de42968c497b0e59abeec3023ba debuginfo(build-id) = c4667e632e180f5a5ee79e510f05b49e7f33e3d1 debuginfo(build-id) = d6c4d4a3307af621c0933554275ff012b89e4bd4 debuginfo(build-id) = db9b2c42f9b254bac38e5b124a3597dd8e5e38bb percolator-debuginfo = 3.06.04-5.fc42 percolator-debuginfo(s390-64) = 3.06.04-5.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: percolator-debugsource(s390-64) = 3.06.04-5.fc42
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/percolator-3.06.04-build/BUILDROOT
Wrote: /builddir/build/RPMS/percolator-static-3.06.04-5.fc42.s390x.rpm
Wrote: /builddir/build/RPMS/percolator-3.06.04-5.fc42.s390x.rpm
Wrote: /builddir/build/RPMS/percolator-debugsource-3.06.04-5.fc42.s390x.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.06.04-5.fc42.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.06.04-5.fc42.s390x.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.apuBL8
+ umask 022
+ cd /builddir/build/BUILD/percolator-3.06.04-build
+ test -d /builddir/build/BUILD/percolator-3.06.04-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/percolator-3.06.04-build
+ rm -rf /builddir/build/BUILD/percolator-3.06.04-build
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild percolator-3.06.04-5.fc42.src.rpm
Finish: build phase for percolator-3.06.04-5.fc42.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-s390x-1735115967.112094/root/var/log/dnf5.log
INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz
/bin/tar: Removing leading `/' from member names
INFO: Done(/var/lib/copr-rpmbuild/results/percolator-3.06.04-5.fc42.src.rpm) Config(child) 7 minutes 6 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",
            "epoch": null,
            "version": "3.06.04",
            "release": "5.fc42",
            "arch": "src"
        },
        {
            "name": "percolator-static",
            "epoch": null,
            "version": "3.06.04",
            "release": "5.fc42",
            "arch": "s390x"
        },
        {
            "name": "percolator",
            "epoch": null,
            "version": "3.06.04",
            "release": "5.fc42",
            "arch": "s390x"
        },
        {
            "name": "percolator-debugsource",
            "epoch": null,
            "version": "3.06.04",
            "release": "5.fc42",
            "arch": "s390x"
        },
        {
            "name": "percolator-debuginfo",
            "epoch": null,
            "version": "3.06.04",
            "release": "5.fc42",
            "arch": "s390x"
        },
        {
            "name": "percolator-data",
            "epoch": null,
            "version": "3.06.04",
            "release": "5.fc42",
            "arch": "noarch"
        }
    ]
}
RPMResults finished