Warning: Permanently added '54.174.113.15' (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-aarch64 --chroot fedora-rawhide-aarch64


Version: 1.2
PID: 12516
Logging PID: 12517
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': True,
 'build_id': 8425720,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-aarch64',
 '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-aarch64/',
            '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-aarch64',
 '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-obhqnwg5/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-obhqnwg5/percolator', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-obhqnwg5/percolator'...

Running: git checkout 8d4a914cc97f66bf0ebc9e98e2e65f3401b339ff --

cmd: ['git', 'checkout', '8d4a914cc97f66bf0ebc9e98e2e65f3401b339ff', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-obhqnwg5/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-obhqnwg5/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  22.1M      0 --:--:-- --:--:-- --:--:-- 22.2M
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
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
100 47.9M  100 47.9M    0     0  26.8M      0  0:00:01  0:00:01 --:--:-- 26.8M
INFO: Reading stdout from command: md5sum yeast-01.sqt.tar.gz

Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-obhqnwg5/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-obhqnwg5/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1734739672.320230 -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-obhqnwg5/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-obhqnwg5/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1734739672.320230 -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-obhqnwg5/percolator/percolator.spec)  Config(fedora-rawhide-aarch64)
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-aarch64-bootstrap-1734739672.320230/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-5761974e-21a0-4e00-ab17-72a4f1989851
INFO: Checking that 5f87c0f1e040f2e2f1e0d50fa9c9806ff92e3b52a45083121db4e7c4f53e5107 image matches host's architecture
INFO: Copy content of container 5f87c0f1e040f2e2f1e0d50fa9c9806ff92e3b52a45083121db4e7c4f53e5107 to /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1734739672.320230/root
INFO: mounting 5f87c0f1e040f2e2f1e0d50fa9c9806ff92e3b52a45083121db4e7c4f53e5107 with podman image mount
INFO: image 5f87c0f1e040f2e2f1e0d50fa9c9806ff92e3b52a45083121db4e7c4f53e5107 as /var/lib/containers/storage/overlay/bad9e80acbd741d5eaa99edcba5ef7ce2477d3046d41b3e7379d9b3d31adec85/merged
INFO: umounting image 5f87c0f1e040f2e2f1e0d50fa9c9806ff92e3b52a45083121db4e7c4f53e5107 (/var/lib/containers/storage/overlay/bad9e80acbd741d5eaa99edcba5ef7ce2477d3046d41b3e7379d9b3d31adec85/merged) with podman image umount
INFO: Removing image mock-bootstrap-5761974e-21a0-4e00-ab17-72a4f1989851
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-aarch64-1734739672.320230/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.aarch64
  rpm-sequoia-1.7.0-3.fc42.aarch64
  dnf5-5.2.8.1-2.fc42.aarch64
  dnf5-plugins-5.2.8.1-2.fc42.aarch64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 fedora                                 100% |  28.9 MiB/s |  20.7 MiB |  00m01s
 Copr repository                        100% |  62.5 MiB/s |   6.5 MiB |  00m00s
 Additional repo https_fedorapeople_org 100% | 110.4 KiB/s |  15.9 KiB |  00m00s
Repositories loaded.
Package                            Arch    Version                    Repository                                                             Size
Installing group/module packages:
 bash                              aarch64 5.2.37-1.fc42              fedora                                                              8.2 MiB
 bzip2                             aarch64 1.0.8-19.fc42              copr_base                                                         168.7 KiB
 coreutils                         aarch64 9.5-11.fc42                copr_base                                                           7.9 MiB
 cpio                              aarch64 2.15-2.fc41                fedora                                                              1.2 MiB
 diffutils                         aarch64 3.10-8.fc42                copr_base                                                           1.7 MiB
 fedora-release-common             noarch  42-0.11                    fedora                                                             19.8 KiB
 findutils                         aarch64 1:4.10.0-4.fc42            copr_base                                                           1.9 MiB
 gawk                              aarch64 5.3.0-4.fc41               fedora                                                              4.2 MiB
 glibc-minimal-langpack            aarch64 2.40.9000-24.fc42          copr_base                                                           0.0   B
 grep                              aarch64 3.11-9.fc42                copr_base                                                           1.0 MiB
 gzip                              aarch64 1.13-2.fc42                copr_base                                                         422.7 KiB
 info                              aarch64 7.1.1-2.fc42               fedora                                                            613.6 KiB
 patch                             aarch64 2.7.6-25.fc42              copr_base                                                         259.0 KiB
 redhat-rpm-config                 noarch  300-1.no_annobin.0.fc42    copr_base                                                         186.6 KiB
 rpm-build                         aarch64 4.20.0-1.fc42              fedora                                                              1.4 MiB
 sed                               aarch64 4.9-3.fc41                 fedora                                                              1.0 MiB
 shadow-utils                      aarch64 2:4.17.0~rc1-1.fc42        fedora                                                              4.5 MiB
 tar                               aarch64 2:1.35-4.fc41              fedora                                                              3.1 MiB
 unzip                             aarch64 6.0-65.fc42                fedora                                                              2.3 MiB
 util-linux                        aarch64 2.40.2-8.fc42              fedora                                                             16.9 MiB
 which                             aarch64 2.21-42.fc41               fedora                                                            248.2 KiB
 xz                                aarch64 1:5.6.3-2.fc42             fedora                                                              1.5 MiB
Installing dependencies:
 add-determinism                   aarch64 0.4.3-1.fc42               fedora                                                              2.1 MiB
 alternatives                      aarch64 1.31-1.fc42                fedora                                                             88.7 KiB
 ansible-srpm-macros               noarch  1-16.fc41                  fedora                                                             35.7 KiB
 audit-libs                        aarch64 4.0.2-1.fc42               copr_base                                                         415.2 KiB
 authselect                        aarch64 1.5.0-8.fc42               copr_base                                                         179.9 KiB
 authselect-libs                   aarch64 1.5.0-8.fc42               copr_base                                                         865.5 KiB
 basesystem                        noarch  11-21.fc41                 fedora                                                              0.0   B
 binutils                          aarch64 2.43.50-9.fc42             copr_base                                                          28.9 MiB
 build-reproducibility-srpm-macros noarch  0.4.3-1.fc42               fedora                                                            735.0   B
 bzip2-libs                        aarch64 1.0.8-19.fc42              copr_base                                                         135.1 KiB
 ca-certificates                   noarch  2024.2.69_v8.0.401-3.fc42  fedora                                                              2.6 MiB
 coreutils-common                  aarch64 9.5-11.fc42                copr_base                                                          11.2 MiB
 cracklib                          aarch64 2.9.11-6.fc42              copr_base                                                         417.7 KiB
 crypto-policies                   noarch  20241128-1.gitbb7b0b0.fc42 fedora                                                            137.3 KiB
 curl                              aarch64 8.11.1-2.fc42              copr_base                                                         451.9 KiB
 cyrus-sasl-lib                    aarch64 2.1.28-27.fc41             fedora                                                              3.1 MiB
 debugedit                         aarch64 5.1-2.fc42                 copr_base                                                         241.5 KiB
 dwz                               aarch64 0.15-8.fc42                copr_base                                                         319.6 KiB
 ed                                aarch64 1.20.2-2.fc41              fedora                                                            282.8 KiB
 efi-srpm-macros                   noarch  5-13.fc42                  fedora                                                             40.2 KiB
 elfutils                          aarch64 0.192-7.fc42               copr_base                                                           3.0 MiB
 elfutils-debuginfod-client        aarch64 0.192-7.fc42               copr_base                                                         141.3 KiB
 elfutils-default-yama-scope       noarch  0.192-7.fc42               copr_base                                                           1.8 KiB
 elfutils-libelf                   aarch64 0.192-7.fc42               copr_base                                                           1.2 MiB
 elfutils-libs                     aarch64 0.192-7.fc42               copr_base                                                         734.9 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                              aarch64 5.45-8.fc42                fedora                                                            139.5 KiB
 file-libs                         aarch64 5.45-8.fc42                fedora                                                             10.0 MiB
 filesystem                        aarch64 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                       aarch64 15.2-4.fc42                copr_base                                                          12.6 MiB
 gdbm                              aarch64 1:1.23-7.fc41              fedora                                                            928.5 KiB
 gdbm-libs                         aarch64 1:1.23-7.fc41              fedora                                                            426.0 KiB
 ghc-srpm-macros                   noarch  1.9.2-1.fc42               fedora                                                            779.0   B
 glibc                             aarch64 2.40.9000-24.fc42          copr_base                                                           6.0 MiB
 glibc-common                      aarch64 2.40.9000-24.fc42          copr_base                                                           1.3 MiB
 glibc-gconv-extra                 aarch64 2.40.9000-24.fc42          copr_base                                                          18.3 MiB
 gmp                               aarch64 1:6.3.0-2.fc41             fedora                                                            722.0 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                           aarch64 2.14-1.fc42                copr_base                                                          90.8 KiB
 json-c                            aarch64 0.18-1.fc42                copr_base                                                         135.7 KiB
 kernel-srpm-macros                noarch  1.0-24.fc41                fedora                                                              1.9 KiB
 keyutils-libs                     aarch64 1.6.3-4.fc42               copr_base                                                          96.8 KiB
 krb5-libs                         aarch64 1.21.3-3.fc42              copr_base                                                           2.5 MiB
 libacl                            aarch64 2.3.2-2.fc42               copr_base                                                          66.3 KiB
 libarchive                        aarch64 3.7.7-1.fc42               copr_base                                                         899.2 KiB
 libattr                           aarch64 2.5.2-4.fc41               fedora                                                            196.6 KiB
 libblkid                          aarch64 2.40.2-8.fc42              fedora                                                            418.6 KiB
 libbrotli                         aarch64 1.1.0-5.fc42               copr_base                                                         904.3 KiB
 libcap                            aarch64 2.71-1.fc42                copr_base                                                         498.5 KiB
 libcap-ng                         aarch64 0.8.5-3.fc42               copr_base                                                         158.7 KiB
 libcom_err                        aarch64 1.47.1-6.fc42              fedora                                                            239.3 KiB
 libcurl                           aarch64 8.11.1-2.fc42              copr_base                                                         845.2 KiB
 libeconf                          aarch64 0.7.5-1.fc42               copr_base                                                          78.7 KiB
 libevent                          aarch64 2.1.12-14.fc42             copr_base                                                           1.1 MiB
 libfdisk                          aarch64 2.40.2-8.fc42              fedora                                                            482.9 KiB
 libffi                            aarch64 3.4.6-3.fc42               fedora                                                            282.4 KiB
 libgcc                            aarch64 15.0.0-0.2.fc42            https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 218.8 KiB
 libgomp                           aarch64 15.0.0-0.2.fc42            https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 501.0 KiB
 libidn2                           aarch64 2.3.7-2.fc42               copr_base                                                         327.7 KiB
 libmount                          aarch64 2.40.2-8.fc42              fedora                                                            483.9 KiB
 libnghttp2                        aarch64 1.64.0-1.fc42              fedora                                                            262.2 KiB
 libnsl2                           aarch64 2.0.1-2.fc42               copr_base                                                          92.3 KiB
 libpkgconf                        aarch64 2.3.0-1.fc42               fedora                                                            198.1 KiB
 libpsl                            aarch64 0.21.5-4.fc42              copr_base                                                         131.2 KiB
 libpwquality                      aarch64 1.4.5-11.fc42              copr_base                                                         604.7 KiB
 libselinux                        aarch64 3.8-0.rc3.1.fc42           fedora                                                            195.6 KiB
 libsemanage                       aarch64 3.8-0.rc3.1.fc42           fedora                                                            353.3 KiB
 libsepol                          aarch64 3.8-0.rc3.1.fc42           fedora                                                            796.3 KiB
 libsmartcols                      aarch64 2.40.2-8.fc42              fedora                                                            288.5 KiB
 libssh                            aarch64 0.11.1-1.fc42              copr_base                                                         575.7 KiB
 libssh-config                     noarch  0.11.1-1.fc42              copr_base                                                         277.0   B
 libstdc++                         aarch64 15.0.0-0.2.fc42            https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch   2.7 MiB
 libtasn1                          aarch64 4.19.0-9.fc42              copr_base                                                         217.7 KiB
 libtirpc                          aarch64 1.3.6-1.fc42               fedora                                                            212.9 KiB
 libtool-ltdl                      aarch64 2.5.4-1.fc42               copr_base                                                          92.1 KiB
 libunistring                      aarch64 1.1-8.fc42                 copr_base                                                           1.7 MiB
 libuuid                           aarch64 2.40.2-8.fc42              fedora                                                            197.5 KiB
 libverto                          aarch64 0.3.2-9.fc41               fedora                                                            197.5 KiB
 libxcrypt                         aarch64 4.4.36-11.fc42             fedora                                                            271.5 KiB
 libxml2                           aarch64 2.12.8-2.fc42              copr_base                                                           1.9 MiB
 libzstd                           aarch64 1.5.6-2.fc41               fedora                                                            796.0 KiB
 lua-libs                          aarch64 5.4.7-1.fc42               fedora                                                            393.1 KiB
 lua-srpm-macros                   noarch  1-14.fc41                  fedora                                                              1.3 KiB
 lz4-libs                          aarch64 1.10.0-1.fc42              copr_base                                                         195.5 KiB
 mpfr                              aarch64 4.2.1-5.fc42               copr_base                                                         748.3 KiB
 ncurses-base                      noarch  6.5-2.20240629.fc41        fedora                                                            326.3 KiB
 ncurses-libs                      aarch64 6.5-2.20240629.fc41        fedora                                                              2.2 MiB
 ocaml-srpm-macros                 noarch  10-3.fc41                  fedora                                                              1.9 KiB
 openblas-srpm-macros              noarch  2-18.fc41                  fedora                                                            112.0   B
 openldap                          aarch64 2.6.8-6.fc42               copr_base                                                         747.0 KiB
 openssl-libs                      aarch64 1:3.2.2-8.fc42             copr_base                                                           6.3 MiB
 p11-kit                           aarch64 0.25.5-4.fc42              copr_base                                                           2.3 MiB
 p11-kit-trust                     aarch64 0.25.5-4.fc42              copr_base                                                         456.7 KiB
 package-notes-srpm-macros         noarch  0.5-12.fc41                fedora                                                              1.6 KiB
 pam                               aarch64 1.7.0-3.fc42               copr_base                                                           4.2 MiB
 pam-libs                          aarch64 1.7.0-3.fc42               copr_base                                                         218.7 KiB
 pcre2                             aarch64 10.44-1.fc42.1             copr_base                                                         644.5 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                           aarch64 2.3.0-1.fc42               fedora                                                            240.6 KiB
 pkgconf-m4                        noarch  2.3.0-1.fc42               fedora                                                             14.4 KiB
 pkgconf-pkg-config                aarch64 2.3.0-1.fc42               fedora                                                            990.0   B
 popt                              aarch64 1.19-7.fc41                fedora                                                            272.9 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                          aarch64 8.2-11.fc42                fedora                                                            753.3 KiB
 rpm                               aarch64 4.20.0-1.fc42              fedora                                                              3.9 MiB
 rpm-build-libs                    aarch64 4.20.0-1.fc42              fedora                                                            262.7 KiB
 rpm-libs                          aarch64 4.20.0-1.fc42              fedora                                                            797.9 KiB
 rpm-sequoia                       aarch64 1.7.0-3.fc42               fedora                                                              2.2 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                       aarch64 3.47.2-1.fc42              fedora                                                              1.4 MiB
 systemd-libs                      aarch64 257-1.fc42                 fedora                                                              2.4 MiB
 util-linux-core                   aarch64 2.40.2-8.fc42              fedora                                                              6.2 MiB
 xxhash-libs                       aarch64 0.8.2-4.fc42               fedora                                                            212.3 KiB
 xz-libs                           aarch64 1:5.6.3-2.fc42             fedora                                                            266.4 KiB
 zig-srpm-macros                   noarch  1-3.fc41                   fedora                                                              1.1 KiB
 zip                               aarch64 3.0-42.fc42                fedora                                                            755.7 KiB
 zlib-ng-compat                    aarch64 2.2.2-1.fc42               fedora                                                            133.8 KiB
 zstd                              aarch64 1.5.6-2.fc41               fedora                                                              1.7 MiB
Installing groups:
 Buildsystem building group                                                                                                                      

Transaction Summary:
 Installing:       155 packages

Total size of inbound packages is 50 MiB. Need to download 50 MiB.
After this operation, 229 MiB extra will be used (install 229 MiB, remove 0 B).
[  1/155] fedora-release-common-0:42-0. 100% |   1.8 MiB/s |  23.9 KiB |  00m00s
[  2/155] cpio-0:2.15-2.fc41.aarch64    100% |  17.8 MiB/s | 291.3 KiB |  00m00s
[  3/155] bash-0:5.2.37-1.fc42.aarch64  100% |  89.6 MiB/s |   1.8 MiB |  00m00s
[  4/155] gawk-0:5.3.0-4.fc41.aarch64   100% | 117.5 MiB/s |   1.1 MiB |  00m00s
[  5/155] info-0:7.1.1-2.fc42.aarch64   100% |  25.3 MiB/s | 181.3 KiB |  00m00s
[  6/155] rpm-build-0:4.20.0-1.fc42.aar 100% |  20.5 MiB/s |  84.1 KiB |  00m00s
[  7/155] sed-0:4.9-3.fc41.aarch64      100% |  61.6 MiB/s | 315.4 KiB |  00m00s
[  8/155] tar-2:1.35-4.fc41.aarch64     100% | 104.3 MiB/s | 854.7 KiB |  00m00s
[  9/155] shadow-utils-2:4.17.0~rc1-1.f 100% | 106.7 MiB/s |   1.3 MiB |  00m00s
[ 10/155] unzip-0:6.0-65.fc42.aarch64   100% |  18.1 MiB/s | 185.5 KiB |  00m00s
[ 11/155] which-0:2.21-42.fc41.aarch64  100% |   6.7 MiB/s |  41.5 KiB |  00m00s
[ 12/155] util-linux-0:2.40.2-8.fc42.aa 100% | 106.6 MiB/s |   1.2 MiB |  00m00s
[ 13/155] xz-1:5.6.3-2.fc42.aarch64     100% |  51.7 MiB/s | 476.1 KiB |  00m00s
[ 14/155] bzip2-0:1.0.8-19.fc42.aarch64 100% |   5.4 MiB/s |  50.0 KiB |  00m00s
[ 15/155] diffutils-0:3.10-8.fc42.aarch 100% |  47.3 MiB/s | 387.7 KiB |  00m00s
[ 16/155] coreutils-0:9.5-11.fc42.aarch 100% |  69.2 MiB/s | 920.7 KiB |  00m00s
[ 17/155] findutils-1:4.10.0-4.fc42.aar 100% |  58.7 MiB/s | 541.0 KiB |  00m00s
[ 18/155] glibc-minimal-langpack-0:2.40 100% |  23.9 MiB/s | 122.4 KiB |  00m00s
[ 19/155] grep-0:3.11-9.fc42.aarch64    100% |  55.7 MiB/s | 285.2 KiB |  00m00s
[ 20/155] gzip-0:1.13-2.fc42.aarch64    100% |  39.3 MiB/s | 161.1 KiB |  00m00s
[ 21/155] redhat-rpm-config-0:300-1.no_ 100% |  37.4 MiB/s |  76.6 KiB |  00m00s
[ 22/155] patch-0:2.7.6-25.fc42.aarch64 100% |  30.2 MiB/s | 123.7 KiB |  00m00s
[ 23/155] fedora-repos-0:42-0.3.noarch  100% |   9.0 MiB/s |   9.2 KiB |  00m00s
[ 24/155] ncurses-libs-0:6.5-2.20240629 100% |  79.7 MiB/s | 326.5 KiB |  00m00s
[ 25/155] filesystem-0:3.18-29.fc42.aar 100% | 135.8 MiB/s |   1.1 MiB |  00m00s
[ 26/155] gmp-1:6.3.0-2.fc41.aarch64    100% |  44.0 MiB/s | 270.1 KiB |  00m00s
[ 27/155] readline-0:8.2-11.fc42.aarch6 100% |  41.6 MiB/s | 212.7 KiB |  00m00s
[ 28/155] file-0:5.45-8.fc42.aarch64    100% |  23.9 MiB/s |  49.0 KiB |  00m00s
[ 29/155] pkgconf-pkg-config-0:2.3.0-1. 100% |   4.9 MiB/s |  10.0 KiB |  00m00s
[ 30/155] popt-0:1.19-7.fc41.aarch64    100% |  32.2 MiB/s |  66.0 KiB |  00m00s
[ 31/155] rpm-build-libs-0:4.20.0-1.fc4 100% |  46.4 MiB/s |  95.1 KiB |  00m00s
[ 32/155] rpm-0:4.20.0-1.fc42.aarch64   100% | 134.0 MiB/s | 549.0 KiB |  00m00s
[ 33/155] rpm-libs-0:4.20.0-1.fc42.aarc 100% |  49.3 MiB/s | 302.8 KiB |  00m00s
[ 34/155] libattr-0:2.5.2-4.fc41.aarch6 100% |   3.6 MiB/s |  18.2 KiB |  00m00s
[ 35/155] zstd-0:1.5.6-2.fc41.aarch64   100% |  74.4 MiB/s | 456.8 KiB |  00m00s
[ 36/155] libxcrypt-0:4.4.36-11.fc42.aa 100% |  23.9 MiB/s | 122.4 KiB |  00m00s
[ 37/155] setup-0:2.15.0-5.fc41.noarch  100% |  30.2 MiB/s | 154.4 KiB |  00m00s
[ 38/155] libblkid-0:2.40.2-8.fc42.aarc 100% |  24.3 MiB/s | 124.3 KiB |  00m00s
[ 39/155] libfdisk-0:2.40.2-8.fc42.aarc 100% |  50.7 MiB/s | 155.7 KiB |  00m00s
[ 40/155] libsmartcols-0:2.40.2-8.fc42. 100% |  40.5 MiB/s |  82.9 KiB |  00m00s
[ 41/155] libmount-0:2.40.2-8.fc42.aarc 100% |  37.7 MiB/s | 154.6 KiB |  00m00s
[ 42/155] libuuid-0:2.40.2-8.fc42.aarch 100% |  28.8 MiB/s |  29.5 KiB |  00m00s
[ 43/155] zlib-ng-compat-0:2.2.2-1.fc42 100% |  32.1 MiB/s |  65.7 KiB |  00m00s
[ 44/155] systemd-libs-0:257-1.fc42.aar 100% | 146.4 MiB/s | 749.6 KiB |  00m00s
[ 45/155] util-linux-core-0:2.40.2-8.fc 100% |  86.6 MiB/s | 532.1 KiB |  00m00s
[ 46/155] xz-libs-1:5.6.3-2.fc42.aarch6 100% |  36.2 MiB/s | 111.1 KiB |  00m00s
[ 47/155] ed-0:1.20.2-2.fc41.aarch64    100% |  39.6 MiB/s |  81.2 KiB |  00m00s
[ 48/155] ansible-srpm-macros-0:1-16.fc 100% |  20.3 MiB/s |  20.8 KiB |  00m00s
[ 49/155] build-reproducibility-srpm-ma 100% |  10.9 MiB/s |  11.2 KiB |  00m00s
[ 50/155] filesystem-srpm-macros-0:3.18 100% |  23.3 MiB/s |  23.9 KiB |  00m00s
[ 51/155] efi-srpm-macros-0:5-13.fc42.n 100% |  11.0 MiB/s |  22.5 KiB |  00m00s
[ 52/155] fonts-srpm-macros-1:2.0.5-17. 100% |  13.2 MiB/s |  27.0 KiB |  00m00s
[ 53/155] fpc-srpm-macros-0:1.3-13.fc41 100% |   7.8 MiB/s |   8.0 KiB |  00m00s
[ 54/155] forge-srpm-macros-0:0.4.0-1.f 100% |   9.6 MiB/s |  19.8 KiB |  00m00s
[ 55/155] ghc-srpm-macros-0:1.9.2-1.fc4 100% |   8.9 MiB/s |   9.1 KiB |  00m00s
[ 56/155] gnat-srpm-macros-0:6-6.fc41.n 100% |   8.7 MiB/s |   9.0 KiB |  00m00s
[ 57/155] go-srpm-macros-0:3.6.0-5.fc42 100% |  27.3 MiB/s |  28.0 KiB |  00m00s
[ 58/155] kernel-srpm-macros-0:1.0-24.f 100% |   4.8 MiB/s |   9.9 KiB |  00m00s
[ 59/155] lua-srpm-macros-0:1-14.fc41.n 100% |   4.3 MiB/s |   8.9 KiB |  00m00s
[ 60/155] ocaml-srpm-macros-0:10-3.fc41 100% |   4.5 MiB/s |   9.2 KiB |  00m00s
[ 61/155] openblas-srpm-macros-0:2-18.f 100% |   7.5 MiB/s |   7.7 KiB |  00m00s
[ 62/155] package-notes-srpm-macros-0:0 100% |   9.6 MiB/s |   9.8 KiB |  00m00s
[ 63/155] perl-srpm-macros-0:1-56.fc41. 100% |   8.3 MiB/s |   8.5 KiB |  00m00s
[ 64/155] pyproject-srpm-macros-0:1.16. 100% |  13.5 MiB/s |  13.9 KiB |  00m00s
[ 65/155] python-srpm-macros-0:3.13-3.f 100% |  23.2 MiB/s |  23.7 KiB |  00m00s
[ 66/155] qt5-srpm-macros-0:5.15.15-1.f 100% |   8.7 MiB/s |   8.9 KiB |  00m00s
[ 67/155] qt6-srpm-macros-0:6.8.1-4.fc4 100% |   9.1 MiB/s |   9.3 KiB |  00m00s
[ 68/155] rust-srpm-macros-0:26.3-3.fc4 100% |  11.8 MiB/s |  12.1 KiB |  00m00s
[ 69/155] zig-srpm-macros-0:1-3.fc41.no 100% |   7.9 MiB/s |   8.1 KiB |  00m00s
[ 70/155] zip-0:3.0-42.fc42.aarch64     100% |  83.0 MiB/s | 255.1 KiB |  00m00s
[ 71/155] ncurses-base-0:6.5-2.20240629 100% |  28.8 MiB/s |  88.4 KiB |  00m00s
[ 72/155] fedora-gpg-keys-0:42-0.3.noar 100% |  43.5 MiB/s | 133.6 KiB |  00m00s
[ 73/155] fedora-repos-rawhide-0:42-0.3 100% |   4.3 MiB/s |   8.8 KiB |  00m00s
[ 74/155] pkgconf-m4-0:2.3.0-1.fc42.noa 100% |   7.0 MiB/s |  14.3 KiB |  00m00s
[ 75/155] pkgconf-0:2.3.0-1.fc42.aarch6 100% |  22.1 MiB/s |  45.2 KiB |  00m00s
[ 76/155] file-libs-0:5.45-8.fc42.aarch 100% | 148.7 MiB/s | 761.3 KiB |  00m00s
[ 77/155] lua-libs-0:5.4.7-1.fc42.aarch 100% |  63.3 MiB/s | 129.7 KiB |  00m00s
[ 78/155] libzstd-0:1.5.6-2.fc41.aarch6 100% |  93.7 MiB/s | 288.0 KiB |  00m00s
[ 79/155] rpm-sequoia-0:1.7.0-3.fc42.aa 100% | 127.4 MiB/s | 782.6 KiB |  00m00s
[ 80/155] sqlite-libs-0:3.47.2-1.fc42.a 100% |  95.8 MiB/s | 686.5 KiB |  00m00s
[ 81/155] add-determinism-0:0.4.3-1.fc4 100% | 102.7 MiB/s | 841.1 KiB |  00m00s
[ 82/155] libpkgconf-0:2.3.0-1.fc42.aar 100% |  12.5 MiB/s |  38.4 KiB |  00m00s
[ 83/155] basesystem-0:11-21.fc41.noarc 100% |   7.2 MiB/s |   7.4 KiB |  00m00s
[ 84/155] dwz-0:0.15-8.fc42.aarch64     100% |  44.1 MiB/s | 135.4 KiB |  00m00s
[ 85/155] libselinux-0:3.8-0.rc3.1.fc42 100% |  44.3 MiB/s |  90.7 KiB |  00m00s
[ 86/155] libsepol-0:3.8-0.rc3.1.fc42.a 100% |  77.4 MiB/s | 316.9 KiB |  00m00s
[ 87/155] glibc-0:2.40.9000-24.fc42.aar 100% | 164.4 MiB/s |   1.8 MiB |  00m00s
[ 88/155] pcre2-0:10.44-1.fc42.1.aarch6 100% |  31.2 MiB/s | 223.9 KiB |  00m00s
[ 89/155] pcre2-syntax-0:10.44-1.fc42.1 100% |  24.5 MiB/s | 150.4 KiB |  00m00s
[ 90/155] glibc-common-0:2.40.9000-24.f 100% |  93.1 MiB/s | 381.2 KiB |  00m00s
[ 91/155] elfutils-libelf-0:0.192-7.fc4 100% |  50.2 MiB/s | 205.7 KiB |  00m00s
[ 92/155] libacl-0:2.3.2-2.fc42.aarch64 100% |   7.6 MiB/s |  23.4 KiB |  00m00s
[ 93/155] libcap-0:2.71-1.fc42.aarch64  100% |  38.3 MiB/s |  78.4 KiB |  00m00s
[ 94/155] coreutils-common-0:9.5-11.fc4 100% | 174.8 MiB/s |   2.1 MiB |  00m00s
[ 95/155] ca-certificates-0:2024.2.69_v 100% | 131.8 MiB/s | 944.5 KiB |  00m00s
[ 96/155] openssl-libs-1:3.2.2-8.fc42.a 100% | 159.7 MiB/s |   2.1 MiB |  00m00s
[ 97/155] crypto-policies-0:20241128-1. 100% |  32.0 MiB/s |  98.4 KiB |  00m00s
[ 98/155] libffi-0:3.4.6-3.fc42.aarch64 100% |  37.4 MiB/s |  38.3 KiB |  00m00s
[ 99/155] bzip2-libs-0:1.0.8-19.fc42.aa 100% |  41.7 MiB/s |  42.7 KiB |  00m00s
[100/155] lz4-libs-0:1.10.0-1.fc42.aarc 100% |  77.5 MiB/s |  79.3 KiB |  00m00s
[101/155] audit-libs-0:4.0.2-1.fc42.aar 100% |  40.4 MiB/s | 124.0 KiB |  00m00s
[102/155] authselect-libs-0:1.5.0-8.fc4 100% |  98.8 MiB/s | 202.3 KiB |  00m00s
[103/155] libcap-ng-0:0.8.5-3.fc42.aarc 100% |  10.1 MiB/s |  30.9 KiB |  00m00s
[104/155] pam-0:1.7.0-3.fc42.aarch64    100% | 114.7 MiB/s | 469.6 KiB |  00m00s
[105/155] gdbm-1:1.23-7.fc41.aarch64    100% |  49.3 MiB/s | 151.6 KiB |  00m00s
[106/155] gdbm-libs-1:1.23-7.fc41.aarch 100% |  27.5 MiB/s |  56.3 KiB |  00m00s
[107/155] libtirpc-0:1.3.6-1.fc42.aarch 100% |  46.6 MiB/s |  95.4 KiB |  00m00s
[108/155] libcom_err-0:1.47.1-6.fc42.aa 100% |  26.3 MiB/s |  26.9 KiB |  00m00s
[109/155] pam-libs-0:1.7.0-3.fc42.aarch 100% |  26.7 MiB/s |  54.7 KiB |  00m00s
[110/155] libeconf-0:0.7.5-1.fc42.aarch 100% |  33.2 MiB/s |  34.0 KiB |  00m00s
[111/155] libsemanage-0:3.8-0.rc3.1.fc4 100% |  36.6 MiB/s | 112.3 KiB |  00m00s
[112/155] elfutils-libs-0:0.192-7.fc42. 100% |  82.2 MiB/s | 252.4 KiB |  00m00s
[113/155] libgcc-0:15.0.0-0.2.fc42.aarc 100% | 935.6 KiB/s |  89.8 KiB |  00m00s
[114/155] binutils-0:2.43.50-9.fc42.aar 100% | 248.8 MiB/s |   6.0 MiB |  00m00s
[115/155] debugedit-0:5.1-2.fc42.aarch6 100% |  74.7 MiB/s |  76.5 KiB |  00m00s
[116/155] elfutils-0:0.192-7.fc42.aarch 100% | 160.7 MiB/s | 493.8 KiB |  00m00s
[117/155] libarchive-0:3.7.7-1.fc42.aar 100% | 129.9 MiB/s | 399.1 KiB |  00m00s
[118/155] curl-0:8.11.1-2.fc42.aarch64  100% |  70.7 MiB/s | 217.3 KiB |  00m00s
[119/155] krb5-libs-0:1.21.3-3.fc42.aar 100% | 177.6 MiB/s | 727.4 KiB |  00m00s
[120/155] libverto-0:0.3.2-9.fc41.aarch 100% |  20.5 MiB/s |  20.9 KiB |  00m00s
[121/155] mpfr-0:4.2.1-5.fc42.aarch64   100% | 105.2 MiB/s | 323.2 KiB |  00m00s
[122/155] p11-kit-0:0.25.5-4.fc42.aarch 100% |  99.1 MiB/s | 406.1 KiB |  00m00s
[123/155] p11-kit-trust-0:0.25.5-4.fc42 100% |  41.4 MiB/s | 127.1 KiB |  00m00s
[124/155] glibc-gconv-extra-0:2.40.9000 100% | 190.3 MiB/s |   1.5 MiB |  00m00s
[125/155] authselect-0:1.5.0-8.fc42.aar 100% |  68.5 MiB/s | 140.4 KiB |  00m00s
[126/155] libnsl2-0:2.0.1-2.fc42.aarch6 100% |  14.1 MiB/s |  28.8 KiB |  00m00s
[127/155] libpwquality-0:1.4.5-11.fc42. 100% |  50.9 MiB/s | 104.3 KiB |  00m00s
[128/155] alternatives-0:1.31-1.fc42.aa 100% |   9.4 MiB/s |  38.5 KiB |  00m00s
[129/155] libtasn1-0:4.19.0-9.fc42.aarc 100% |  35.1 MiB/s |  71.9 KiB |  00m00s
[130/155] cracklib-0:2.9.11-6.fc42.aarc 100% |  75.7 MiB/s |  77.5 KiB |  00m00s
[131/155] libxml2-0:2.12.8-2.fc42.aarch 100% | 107.0 MiB/s | 657.2 KiB |  00m00s
[132/155] keyutils-libs-0:1.6.3-4.fc42. 100% |  10.0 MiB/s |  30.8 KiB |  00m00s
[133/155] elfutils-default-yama-scope-0 100% |   6.3 MiB/s |  13.0 KiB |  00m00s
[134/155] elfutils-debuginfod-client-0: 100% |  21.5 MiB/s |  44.0 KiB |  00m00s
[135/155] jansson-0:2.14-1.fc42.aarch64 100% |  44.1 MiB/s |  45.2 KiB |  00m00s
[136/155] json-c-0:0.18-1.fc42.aarch64  100% |  41.8 MiB/s |  42.8 KiB |  00m00s
[137/155] fedora-release-0:42-0.11.noar 100% |   2.1 MiB/s |  13.0 KiB |  00m00s
[138/155] gdb-minimal-0:15.2-4.fc42.aar 100% | 245.3 MiB/s |   3.9 MiB |  00m00s
[139/155] libgomp-0:15.0.0-0.2.fc42.aar 100% |   2.1 MiB/s | 322.1 KiB |  00m00s
[140/155] xxhash-libs-0:0.8.2-4.fc42.aa 100% |  16.9 MiB/s |  34.6 KiB |  00m00s
[141/155] fedora-release-identity-basic 100% |  13.5 MiB/s |  13.8 KiB |  00m00s
[142/155] libnghttp2-0:1.64.0-1.fc42.aa 100% |  37.5 MiB/s |  76.8 KiB |  00m00s
[143/155] libcurl-0:8.11.1-2.fc42.aarch 100% | 116.8 MiB/s | 358.9 KiB |  00m00s
[144/155] libbrotli-0:1.1.0-5.fc42.aarc 100% | 110.8 MiB/s | 340.4 KiB |  00m00s
[145/155] libidn2-0:2.3.7-2.fc42.aarch6 100% |  36.4 MiB/s | 111.7 KiB |  00m00s
[146/155] libstdc++-0:15.0.0-0.2.fc42.a 100% |   3.7 MiB/s | 760.1 KiB |  00m00s
[147/155] publicsuffix-list-dafsa-0:202 100% |  28.5 MiB/s |  58.3 KiB |  00m00s
[148/155] libpsl-0:0.21.5-4.fc42.aarch6 100% |  15.6 MiB/s |  63.7 KiB |  00m00s
[149/155] openldap-0:2.6.8-6.fc42.aarch 100% |  58.8 MiB/s | 240.8 KiB |  00m00s
[150/155] libssh-0:0.11.1-1.fc42.aarch6 100% |  31.4 MiB/s | 225.4 KiB |  00m00s
[151/155] cyrus-sasl-lib-0:2.1.28-27.fc 100% | 127.0 MiB/s | 780.2 KiB |  00m00s
[152/155] libevent-0:2.1.12-14.fc42.aar 100% |  78.8 MiB/s | 242.2 KiB |  00m00s
[153/155] libtool-ltdl-0:2.5.4-1.fc42.a 100% |  11.2 MiB/s |  34.3 KiB |  00m00s
[154/155] libssh-config-0:0.11.1-1.fc42 100% |   4.8 MiB/s |   9.9 KiB |  00m00s
[155/155] libunistring-0:1.1-8.fc42.aar 100% | 131.1 MiB/s | 537.0 KiB |  00m00s
--------------------------------------------------------------------------------
[155/155] Total                         100% |  73.7 MiB/s |  50.2 MiB |  00m01s
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.
[  1/157] Verify package files          100% | 685.0   B/s | 155.0   B |  00m00s
>>> Running pre-transaction scriptlet: filesystem-0:3.18-29.fc42.aarch64
>>> Finished pre-transaction scriptlet: filesystem-0:3.18-29.fc42.aarch64
>>> [RPM] /var/lib/mock/fedora-rawhide-aarch64-1734739672.320230/root/var/cache/
[  2/157] Prepare transaction           100% |   2.5 KiB/s | 155.0   B |  00m00s
[  3/157] Installing libgcc-0:15.0.0-0. 100% | 107.7 MiB/s | 220.5 KiB |  00m00s
[  4/157] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
[  5/157] Installing publicsuffix-list- 100% |  66.7 MiB/s |  68.3 KiB |  00m00s
[  6/157] Installing fedora-release-ide 100% |   0.0   B/s | 976.0   B |  00m00s
[  7/157] Installing fedora-repos-rawhi 100% |   2.4 MiB/s |   2.4 KiB |  00m00s
[  8/157] Installing fedora-gpg-keys-0: 100% |  28.0 MiB/s | 172.2 KiB |  00m00s
[  9/157] Installing fedora-repos-0:42- 100% |   0.0   B/s |   5.7 KiB |  00m00s
[ 10/157] Installing fedora-release-com 100% |  23.6 MiB/s |  24.1 KiB |  00m00s
[ 11/157] Installing fedora-release-0:4 100% |   0.0   B/s | 124.0   B |  00m00s
[ 12/157] Installing setup-0:2.15.0-5.f 100% |  44.3 MiB/s | 726.1 KiB |  00m00s
>>> [RPM] /etc/hosts created as /etc/hosts.rpmnew
[ 13/157] Installing filesystem-0:3.18- 100% |   2.5 MiB/s | 212.6 KiB |  00m00s
[ 14/157] Installing basesystem-0:11-21 100% |   0.0   B/s | 124.0   B |  00m00s
[ 15/157] Installing coreutils-common-0 100% | 310.8 MiB/s |  11.2 MiB |  00m00s
[ 16/157] Installing pcre2-syntax-0:10. 100% | 248.1 MiB/s | 254.1 KiB |  00m00s
[ 17/157] Installing pkgconf-m4-0:2.3.0 100% |  14.5 MiB/s |  14.8 KiB |  00m00s
[ 18/157] Installing ncurses-base-0:6.5 100% |  49.1 MiB/s | 351.7 KiB |  00m00s
[ 19/157] Installing glibc-minimal-lang 100% |   0.0   B/s | 124.0   B |  00m00s
[ 20/157] Installing ncurses-libs-0:6.5 100% | 321.2 MiB/s |   2.2 MiB |  00m00s
[ 21/157] Installing glibc-0:2.40.9000- 100% | 261.5 MiB/s |   6.0 MiB |  00m00s
[ 22/157] Installing bash-0:5.2.37-1.fc 100% | 329.2 MiB/s |   8.2 MiB |  00m00s
[ 23/157] Installing glibc-common-0:2.4 100% | 187.2 MiB/s |   1.3 MiB |  00m00s
[ 24/157] Installing glibc-gconv-extra- 100% | 368.7 MiB/s |  18.4 MiB |  00m00s
[ 25/157] Installing zlib-ng-compat-0:2 100% | 131.5 MiB/s | 134.6 KiB |  00m00s
[ 26/157] Installing xz-libs-1:5.6.3-2. 100% | 261.2 MiB/s | 267.5 KiB |  00m00s
[ 27/157] Installing bzip2-libs-0:1.0.8 100% | 133.0 MiB/s | 136.2 KiB |  00m00s
[ 28/157] Installing readline-0:8.2-11. 100% | 245.9 MiB/s | 755.5 KiB |  00m00s
[ 29/157] Installing popt-0:1.19-7.fc41 100% |  91.0 MiB/s | 279.5 KiB |  00m00s
[ 30/157] Installing libuuid-0:2.40.2-8 100% | 194.0 MiB/s | 198.6 KiB |  00m00s
[ 31/157] Installing libblkid-0:2.40.2- 100% | 204.9 MiB/s | 419.7 KiB |  00m00s
[ 32/157] Installing gmp-1:6.3.0-2.fc41 100% | 235.8 MiB/s | 724.2 KiB |  00m00s
[ 33/157] Installing libattr-0:2.5.2-4. 100% | 192.9 MiB/s | 197.5 KiB |  00m00s
[ 34/157] Installing libacl-0:2.3.2-2.f 100% |  65.5 MiB/s |  67.1 KiB |  00m00s
[ 35/157] Installing libxcrypt-0:4.4.36 100% | 133.9 MiB/s | 274.2 KiB |  00m00s
[ 36/157] Installing libzstd-0:1.5.6-2. 100% | 259.5 MiB/s | 797.3 KiB |  00m00s
[ 37/157] Installing elfutils-libelf-0: 100% | 296.6 MiB/s |   1.2 MiB |  00m00s
[ 38/157] Installing libstdc++-0:15.0.0 100% | 300.0 MiB/s |   2.7 MiB |  00m00s
[ 39/157] Installing gdbm-libs-1:1.23-7 100% | 417.7 MiB/s | 427.7 KiB |  00m00s
[ 40/157] Installing libeconf-0:0.7.5-1 100% |  78.5 MiB/s |  80.3 KiB |  00m00s
[ 41/157] Installing dwz-0:0.15-8.fc42. 100% | 156.7 MiB/s | 321.0 KiB |  00m00s
[ 42/157] Installing mpfr-0:4.2.1-5.fc4 100% | 244.1 MiB/s | 749.9 KiB |  00m00s
[ 43/157] Installing gawk-0:5.3.0-4.fc4 100% | 387.6 MiB/s |   4.3 MiB |  00m00s
[ 44/157] Installing unzip-0:6.0-65.fc4 100% | 570.7 MiB/s |   2.3 MiB |  00m00s
[ 45/157] Installing file-libs-0:5.45-8 100% | 586.0 MiB/s |  10.0 MiB |  00m00s
[ 46/157] Installing file-0:5.45-8.fc42 100% |  15.3 MiB/s | 141.0 KiB |  00m00s
[ 47/157] Installing crypto-policies-0: 100% |  20.0 MiB/s | 163.7 KiB |  00m00s
[ 48/157] Installing libsmartcols-0:2.4 100% | 141.4 MiB/s | 289.7 KiB |  00m00s
[ 49/157] Installing lua-libs-0:5.4.7-1 100% | 192.5 MiB/s | 394.3 KiB |  00m00s
[ 50/157] Installing libsepol-0:3.8-0.r 100% | 259.5 MiB/s | 797.2 KiB |  00m00s
[ 51/157] Installing pcre2-0:10.44-1.fc 100% | 315.4 MiB/s | 645.9 KiB |  00m00s
[ 52/157] Installing libselinux-0:3.8-0 100% |  96.1 MiB/s | 196.8 KiB |  00m00s
[ 53/157] Installing sed-0:4.9-3.fc41.a 100% | 164.3 MiB/s |   1.0 MiB |  00m00s
[ 54/157] Installing findutils-1:4.10.0 100% | 239.2 MiB/s |   1.9 MiB |  00m00s
[ 55/157] Installing grep-0:3.11-9.fc42 100% | 147.3 MiB/s |   1.0 MiB |  00m00s
[ 56/157] Installing xz-1:5.6.3-2.fc42. 100% | 188.8 MiB/s |   1.5 MiB |  00m00s
[ 57/157] Installing libmount-0:2.40.2- 100% | 236.8 MiB/s | 485.1 KiB |  00m00s
[ 58/157] Installing libffi-0:3.4.6-3.f 100% | 277.2 MiB/s | 283.8 KiB |  00m00s
[ 59/157] Installing lz4-libs-0:1.10.0- 100% | 192.0 MiB/s | 196.6 KiB |  00m00s
[ 60/157] Installing libcap-ng-0:0.8.5- 100% | 156.8 MiB/s | 160.6 KiB |  00m00s
[ 61/157] Installing audit-libs-0:4.0.2 100% | 203.8 MiB/s | 417.3 KiB |  00m00s
[ 62/157] Installing pam-libs-0:1.7.0-3 100% | 215.9 MiB/s | 221.1 KiB |  00m00s
[ 63/157] Installing libcap-0:2.71-1.fc 100% | 163.9 MiB/s | 503.5 KiB |  00m00s
[ 64/157] Installing systemd-libs-0:257 100% | 302.8 MiB/s |   2.4 MiB |  00m00s
[ 65/157] Installing libcom_err-0:1.47. 100% | 234.8 MiB/s | 240.4 KiB |  00m00s
[ 66/157] Installing alternatives-0:1.3 100% |  88.2 MiB/s |  90.3 KiB |  00m00s
[ 67/157] Installing libtasn1-0:4.19.0- 100% | 107.2 MiB/s | 219.5 KiB |  00m00s
[ 68/157] Installing p11-kit-0:0.25.5-4 100% | 212.7 MiB/s |   2.3 MiB |  00m00s
[ 69/157] Installing libunistring-0:1.1 100% | 290.3 MiB/s |   1.7 MiB |  00m00s
[ 70/157] Installing libidn2-0:2.3.7-2. 100% | 108.6 MiB/s | 333.6 KiB |  00m00s
[ 71/157] Installing libpsl-0:0.21.5-4. 100% | 129.2 MiB/s | 132.3 KiB |  00m00s
[ 72/157] Installing p11-kit-trust-0:0. 100% |  49.7 MiB/s | 458.4 KiB |  00m00s
[ 73/157] Installing openssl-libs-1:3.2 100% | 272.1 MiB/s |   6.3 MiB |  00m00s
[ 74/157] Installing coreutils-0:9.5-11 100% | 247.9 MiB/s |   7.9 MiB |  00m00s
[ 75/157] Installing ca-certificates-0: 100% |   1.4 MiB/s |   2.4 MiB |  00m02s
[ 76/157] Installing gzip-0:1.13-2.fc42 100% | 104.6 MiB/s | 428.3 KiB |  00m00s
[ 77/157] Installing authselect-libs-0: 100% | 122.8 MiB/s | 880.5 KiB |  00m00s
[ 78/157] Installing cracklib-0:2.9.11- 100% |  83.8 MiB/s | 429.0 KiB |  00m00s
[ 79/157] Installing libpwquality-0:1.4 100% | 100.4 MiB/s | 617.1 KiB |  00m00s
[ 80/157] Installing rpm-sequoia-0:1.7. 100% | 277.8 MiB/s |   2.2 MiB |  00m00s
[ 81/157] Installing libevent-0:2.1.12- 100% | 267.3 MiB/s |   1.1 MiB |  00m00s
[ 82/157] Installing util-linux-core-0: 100% | 387.7 MiB/s |   6.2 MiB |  00m00s
[ 83/157] Installing libsemanage-0:3.8- 100% | 115.6 MiB/s | 355.0 KiB |  00m00s
[ 84/157] Installing shadow-utils-2:4.1 100% | 182.5 MiB/s |   4.6 MiB |  00m00s
[ 85/157] Installing zstd-0:1.5.6-2.fc4 100% | 281.8 MiB/s |   1.7 MiB |  00m00s
[ 86/157] Installing tar-2:1.35-4.fc41. 100% | 278.8 MiB/s |   3.1 MiB |  00m00s
[ 87/157] Installing zip-0:3.0-42.fc42. 100% | 185.4 MiB/s | 759.6 KiB |  00m00s
[ 88/157] Installing gdbm-1:1.23-7.fc41 100% | 227.9 MiB/s | 933.4 KiB |  00m00s
[ 89/157] Installing cyrus-sasl-lib-0:2 100% | 345.2 MiB/s |   3.1 MiB |  00m00s
[ 90/157] Installing libfdisk-0:2.40.2- 100% | 236.3 MiB/s | 483.9 KiB |  00m00s
[ 91/157] Installing bzip2-0:1.0.8-19.f 100% |  84.6 MiB/s | 173.2 KiB |  00m00s
[ 92/157] Installing libxml2-0:2.12.8-2 100% | 310.2 MiB/s |   1.9 MiB |  00m00s
[ 93/157] Installing libarchive-0:3.7.7 100% | 220.0 MiB/s | 901.2 KiB |  00m00s
[ 94/157] Installing sqlite-libs-0:3.47 100% | 283.0 MiB/s |   1.4 MiB |  00m00s
[ 95/157] Installing rpm-libs-0:4.20.0- 100% | 260.2 MiB/s | 799.4 KiB |  00m00s
[ 96/157] Installing add-determinism-0: 100% | 299.6 MiB/s |   2.1 MiB |  00m00s
[ 97/157] Installing build-reproducibil 100% |   0.0   B/s |   1.0 KiB |  00m00s
[ 98/157] Installing ed-0:1.20.2-2.fc41 100% | 278.5 MiB/s | 285.1 KiB |  00m00s
[ 99/157] Installing patch-0:2.7.6-25.f 100% | 127.2 MiB/s | 260.5 KiB |  00m00s
[100/157] Installing filesystem-srpm-ma 100% |  35.9 MiB/s |  36.8 KiB |  00m00s
[101/157] Installing elfutils-default-y 100% | 291.9 KiB/s |   2.0 KiB |  00m00s
[102/157] Installing elfutils-libs-0:0. 100% | 179.8 MiB/s | 736.6 KiB |  00m00s
[103/157] Installing cpio-0:2.15-2.fc41 100% | 174.4 MiB/s |   1.2 MiB |  00m00s
[104/157] Installing diffutils-0:3.10-8 100% | 208.0 MiB/s |   1.7 MiB |  00m00s
[105/157] Installing libpkgconf-0:2.3.0 100% | 194.6 MiB/s | 199.2 KiB |  00m00s
[106/157] Installing pkgconf-0:2.3.0-1. 100% | 118.7 MiB/s | 243.1 KiB |  00m00s
[107/157] Installing pkgconf-pkg-config 100% |   0.0   B/s |   1.8 KiB |  00m00s
[108/157] Installing libgomp-0:15.0.0-0 100% | 245.3 MiB/s | 502.4 KiB |  00m00s
[109/157] Installing rpm-build-libs-0:4 100% | 257.4 MiB/s | 263.6 KiB |  00m00s
[110/157] Installing libverto-0:0.3.2-9 100% | 194.7 MiB/s | 199.3 KiB |  00m00s
[111/157] Installing keyutils-libs-0:1. 100% |  95.9 MiB/s |  98.2 KiB |  00m00s
[112/157] Installing krb5-libs-0:1.21.3 100% | 249.7 MiB/s |   2.5 MiB |  00m00s
[113/157] Installing libtirpc-0:1.3.6-1 100% | 209.7 MiB/s | 214.7 KiB |  00m00s
[114/157] Installing libnsl2-0:2.0.1-2. 100% |  91.2 MiB/s |  93.4 KiB |  00m00s
[115/157] Installing pam-0:1.7.0-3.fc42 100% | 201.7 MiB/s |   4.2 MiB |  00m00s
[116/157] Installing libssh-0:0.11.1-1. 100% | 188.1 MiB/s | 577.8 KiB |  00m00s
[117/157] Installing jansson-0:2.14-1.f 100% |  90.0 MiB/s |  92.2 KiB |  00m00s
[118/157] Installing json-c-0:0.18-1.fc 100% | 133.7 MiB/s | 137.0 KiB |  00m00s
[119/157] Installing xxhash-libs-0:0.8. 100% | 208.7 MiB/s | 213.7 KiB |  00m00s
[120/157] Installing libnghttp2-0:1.64. 100% | 257.1 MiB/s | 263.3 KiB |  00m00s
[121/157] Installing libbrotli-0:1.1.0- 100% | 221.3 MiB/s | 906.6 KiB |  00m00s
[122/157] Installing libtool-ltdl-0:2.5 100% |  91.0 MiB/s |  93.2 KiB |  00m00s
[123/157] Installing openldap-0:2.6.8-6 100% | 183.3 MiB/s | 750.8 KiB |  00m00s
[124/157] Installing libcurl-0:8.11.1-2 100% | 275.5 MiB/s | 846.3 KiB |  00m00s
[125/157] Installing elfutils-debuginfo 100% |  70.1 MiB/s | 143.6 KiB |  00m00s
[126/157] Installing binutils-0:2.43.50 100% | 328.3 MiB/s |  28.9 MiB |  00m00s
[127/157] Installing elfutils-0:0.192-7 100% | 275.8 MiB/s |   3.0 MiB |  00m00s
[128/157] Installing gdb-minimal-0:15.2 100% | 307.4 MiB/s |  12.6 MiB |  00m00s
[129/157] Installing debugedit-0:5.1-2. 100% | 119.2 MiB/s | 244.2 KiB |  00m00s
[130/157] Installing curl-0:8.11.1-2.fc 100% |  37.0 MiB/s | 454.4 KiB |  00m00s
[131/157] Installing rpm-0:4.20.0-1.fc4 100% | 152.6 MiB/s |   3.4 MiB |  00m00s
[132/157] Installing efi-srpm-macros-0: 100% |  40.2 MiB/s |  41.2 KiB |  00m00s
[133/157] Installing lua-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[134/157] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.7 KiB |  00m00s
[135/157] Installing rust-srpm-macros-0 100% |   0.0   B/s |   5.6 KiB |  00m00s
[136/157] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 732.0   B |  00m00s
[137/157] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 776.0   B |  00m00s
[138/157] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[139/157] Installing package-notes-srpm 100% |   0.0   B/s |   2.0 KiB |  00m00s
[140/157] Installing openblas-srpm-macr 100% |   0.0   B/s | 392.0   B |  00m00s
[141/157] Installing ocaml-srpm-macros- 100% |   0.0   B/s |   2.2 KiB |  00m00s
[142/157] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[143/157] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[144/157] Installing ghc-srpm-macros-0: 100% |   0.0   B/s |   1.0 KiB |  00m00s
[145/157] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[146/157] Installing ansible-srpm-macro 100% |   0.0   B/s |  36.2 KiB |  00m00s
[147/157] Installing fonts-srpm-macros- 100% |  55.7 MiB/s |  57.0 KiB |  00m00s
[148/157] Installing forge-srpm-macros- 100% |  39.3 MiB/s |  40.3 KiB |  00m00s
[149/157] Installing go-srpm-macros-0:3 100% |  60.5 MiB/s |  62.0 KiB |  00m00s
[150/157] Installing python-srpm-macros 100% |  50.9 MiB/s |  52.2 KiB |  00m00s
[151/157] Installing redhat-rpm-config- 100% |  62.9 MiB/s | 193.2 KiB |  00m00s
[152/157] Installing rpm-build-0:4.20.0 100% | 349.3 MiB/s |   1.4 MiB |  00m00s
[153/157] Installing pyproject-srpm-mac 100% |   1.2 MiB/s |   2.5 KiB |  00m00s
[154/157] Installing util-linux-0:2.40. 100% | 346.0 MiB/s |  17.0 MiB |  00m00s
[155/157] Installing authselect-0:1.5.0 100% |  60.0 MiB/s | 184.3 KiB |  00m00s
[156/157] Installing which-0:2.21-42.fc 100% | 122.2 MiB/s | 250.4 KiB |  00m00s
[157/157] Installing info-0:7.1.1-2.fc4 100% | 286.7 KiB/s | 614.0 KiB |  00m02s
Warning: skipped OpenPGP checks for 63 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-0.4.3-1.fc42.aarch64
alternatives-1.31-1.fc42.aarch64
ansible-srpm-macros-1-16.fc41.noarch
audit-libs-4.0.2-1.fc42.aarch64
authselect-1.5.0-8.fc42.aarch64
authselect-libs-1.5.0-8.fc42.aarch64
basesystem-11-21.fc41.noarch
bash-5.2.37-1.fc42.aarch64
binutils-2.43.50-9.fc42.aarch64
build-reproducibility-srpm-macros-0.4.3-1.fc42.noarch
bzip2-1.0.8-19.fc42.aarch64
bzip2-libs-1.0.8-19.fc42.aarch64
ca-certificates-2024.2.69_v8.0.401-3.fc42.noarch
coreutils-9.5-11.fc42.aarch64
coreutils-common-9.5-11.fc42.aarch64
cpio-2.15-2.fc41.aarch64
cracklib-2.9.11-6.fc42.aarch64
crypto-policies-20241128-1.gitbb7b0b0.fc42.noarch
curl-8.11.1-2.fc42.aarch64
cyrus-sasl-lib-2.1.28-27.fc41.aarch64
debugedit-5.1-2.fc42.aarch64
diffutils-3.10-8.fc42.aarch64
dwz-0.15-8.fc42.aarch64
ed-1.20.2-2.fc41.aarch64
efi-srpm-macros-5-13.fc42.noarch
elfutils-0.192-7.fc42.aarch64
elfutils-debuginfod-client-0.192-7.fc42.aarch64
elfutils-default-yama-scope-0.192-7.fc42.noarch
elfutils-libelf-0.192-7.fc42.aarch64
elfutils-libs-0.192-7.fc42.aarch64
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.aarch64
file-libs-5.45-8.fc42.aarch64
filesystem-3.18-29.fc42.aarch64
filesystem-srpm-macros-3.18-29.fc42.noarch
findutils-4.10.0-4.fc42.aarch64
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.aarch64
gdb-minimal-15.2-4.fc42.aarch64
gdbm-1.23-7.fc41.aarch64
gdbm-libs-1.23-7.fc41.aarch64
ghc-srpm-macros-1.9.2-1.fc42.noarch
glibc-2.40.9000-24.fc42.aarch64
glibc-common-2.40.9000-24.fc42.aarch64
glibc-gconv-extra-2.40.9000-24.fc42.aarch64
glibc-minimal-langpack-2.40.9000-24.fc42.aarch64
gmp-6.3.0-2.fc41.aarch64
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.aarch64
gzip-1.13-2.fc42.aarch64
info-7.1.1-2.fc42.aarch64
jansson-2.14-1.fc42.aarch64
json-c-0.18-1.fc42.aarch64
kernel-srpm-macros-1.0-24.fc41.noarch
keyutils-libs-1.6.3-4.fc42.aarch64
krb5-libs-1.21.3-3.fc42.aarch64
libacl-2.3.2-2.fc42.aarch64
libarchive-3.7.7-1.fc42.aarch64
libattr-2.5.2-4.fc41.aarch64
libblkid-2.40.2-8.fc42.aarch64
libbrotli-1.1.0-5.fc42.aarch64
libcap-2.71-1.fc42.aarch64
libcap-ng-0.8.5-3.fc42.aarch64
libcom_err-1.47.1-6.fc42.aarch64
libcurl-8.11.1-2.fc42.aarch64
libeconf-0.7.5-1.fc42.aarch64
libevent-2.1.12-14.fc42.aarch64
libfdisk-2.40.2-8.fc42.aarch64
libffi-3.4.6-3.fc42.aarch64
libgcc-15.0.0-0.2.fc42.aarch64
libgomp-15.0.0-0.2.fc42.aarch64
libidn2-2.3.7-2.fc42.aarch64
libmount-2.40.2-8.fc42.aarch64
libnghttp2-1.64.0-1.fc42.aarch64
libnsl2-2.0.1-2.fc42.aarch64
libpkgconf-2.3.0-1.fc42.aarch64
libpsl-0.21.5-4.fc42.aarch64
libpwquality-1.4.5-11.fc42.aarch64
libselinux-3.8-0.rc3.1.fc42.aarch64
libsemanage-3.8-0.rc3.1.fc42.aarch64
libsepol-3.8-0.rc3.1.fc42.aarch64
libsmartcols-2.40.2-8.fc42.aarch64
libssh-0.11.1-1.fc42.aarch64
libssh-config-0.11.1-1.fc42.noarch
libstdc++-15.0.0-0.2.fc42.aarch64
libtasn1-4.19.0-9.fc42.aarch64
libtirpc-1.3.6-1.fc42.aarch64
libtool-ltdl-2.5.4-1.fc42.aarch64
libunistring-1.1-8.fc42.aarch64
libuuid-2.40.2-8.fc42.aarch64
libverto-0.3.2-9.fc41.aarch64
libxcrypt-4.4.36-11.fc42.aarch64
libxml2-2.12.8-2.fc42.aarch64
libzstd-1.5.6-2.fc41.aarch64
lua-libs-5.4.7-1.fc42.aarch64
lua-srpm-macros-1-14.fc41.noarch
lz4-libs-1.10.0-1.fc42.aarch64
mpfr-4.2.1-5.fc42.aarch64
ncurses-base-6.5-2.20240629.fc41.noarch
ncurses-libs-6.5-2.20240629.fc41.aarch64
ocaml-srpm-macros-10-3.fc41.noarch
openblas-srpm-macros-2-18.fc41.noarch
openldap-2.6.8-6.fc42.aarch64
openssl-libs-3.2.2-8.fc42.aarch64
p11-kit-0.25.5-4.fc42.aarch64
p11-kit-trust-0.25.5-4.fc42.aarch64
package-notes-srpm-macros-0.5-12.fc41.noarch
pam-1.7.0-3.fc42.aarch64
pam-libs-1.7.0-3.fc42.aarch64
patch-2.7.6-25.fc42.aarch64
pcre2-10.44-1.fc42.1.aarch64
pcre2-syntax-10.44-1.fc42.1.noarch
perl-srpm-macros-1-56.fc41.noarch
pkgconf-2.3.0-1.fc42.aarch64
pkgconf-m4-2.3.0-1.fc42.noarch
pkgconf-pkg-config-2.3.0-1.fc42.aarch64
popt-1.19-7.fc41.aarch64
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.aarch64
redhat-rpm-config-300-1.no_annobin.0.fc42.noarch
rpm-4.20.0-1.fc42.aarch64
rpm-build-4.20.0-1.fc42.aarch64
rpm-build-libs-4.20.0-1.fc42.aarch64
rpm-libs-4.20.0-1.fc42.aarch64
rpm-sequoia-1.7.0-3.fc42.aarch64
rust-srpm-macros-26.3-3.fc42.noarch
sed-4.9-3.fc41.aarch64
setup-2.15.0-5.fc41.noarch
shadow-utils-4.17.0~rc1-1.fc42.aarch64
sqlite-libs-3.47.2-1.fc42.aarch64
systemd-libs-257-1.fc42.aarch64
tar-1.35-4.fc41.aarch64
unzip-6.0-65.fc42.aarch64
util-linux-2.40.2-8.fc42.aarch64
util-linux-core-2.40.2-8.fc42.aarch64
which-2.21-42.fc41.aarch64
xxhash-libs-0.8.2-4.fc42.aarch64
xz-5.6.3-2.fc42.aarch64
xz-libs-5.6.3-2.fc42.aarch64
zig-srpm-macros-1-3.fc41.noarch
zip-3.0-42.fc42.aarch64
zlib-ng-compat-2.2.2-1.fc42.aarch64
zstd-1.5.6-2.fc41.aarch64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: aarch64
Building for target aarch64
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-aarch64-1734739672.320230/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-obhqnwg5/percolator/percolator.spec) Config(child) 0 minutes 26 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-aarch64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1734739672.320230/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1734739672.320230/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-aarch64-1734739672.320230/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.aarch64
  rpm-sequoia-1.7.0-3.fc42.aarch64
  dnf5-5.2.8.1-2.fc42.aarch64
  dnf5-plugins-5.2.8.1-2.fc42.aarch64
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: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1729209600
Wrote: /builddir/build/SRPMS/percolator-3.06.04-5.fc42.src.rpm
Updating and loading repositories:
 Copr repository                        100% | 102.5 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% | 101.4 KiB/s |  11.1 KiB |  00m00s
 Additional repo https_fedorapeople_org 100% |  25.4 KiB/s |   1.5 KiB |  00m00s
Repositories loaded.
Package                    Arch    Version              Repository                                                             Size
Installing:
 boost-devel               aarch64 1.83.0-9.fc42        fedora                                                            143.0 MiB
 boost-static              aarch64 1.83.0-9.fc42        fedora                                                             36.8 MiB
 bzip2-devel               aarch64 1.0.8-19.fc42        copr_base                                                         309.8 KiB
 cmake                     aarch64 3.31.2-1.fc42        copr_base                                                          28.9 MiB
 gcc                       aarch64 15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch  97.8 MiB
 gcc-c++                   aarch64 15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch  38.5 MiB
 gtest-devel               aarch64 1.14.0-5.fc42        copr_base                                                           1.0 MiB
 libtirpc-devel            aarch64 1.3.6-1.fc42         fedora                                                            251.6 KiB
 make                      aarch64 1:4.4.1-9.fc42       copr_base                                                           1.8 MiB
 python3-devel             aarch64 3.13.1-2.fc42        fedora                                                              1.8 MiB
 sqlite-devel              aarch64 3.47.2-1.fc42        fedora                                                            673.4 KiB
 tokyocabinet-devel        aarch64 1.4.48-26.fc41       fedora                                                            460.2 KiB
 xerces-c-devel            aarch64 3.3.0-5.fc42         fedora                                                              4.1 MiB
 xsd                       aarch64 4.1.0-0.16.a11.fc42  fedora                                                              4.7 MiB
 zlib-ng-compat-devel      aarch64 2.2.2-1.fc42         fedora                                                            106.8 KiB
Installing dependencies:
 annobin-docs              noarch  12.79-1.fc42         copr_base                                                          98.6 KiB
 annobin-plugin-gcc        aarch64 12.79-1.fc42         copr_base                                                         997.2 KiB
 boost                     aarch64 1.83.0-9.fc42        fedora                                                              1.3 KiB
 boost-atomic              aarch64 1.83.0-9.fc42        fedora                                                             67.6 KiB
 boost-chrono              aarch64 1.83.0-9.fc42        fedora                                                             67.7 KiB
 boost-container           aarch64 1.83.0-9.fc42        fedora                                                             67.7 KiB
 boost-context             aarch64 1.83.0-9.fc42        fedora                                                             67.4 KiB
 boost-contract            aarch64 1.83.0-9.fc42        fedora                                                            131.8 KiB
 boost-coroutine           aarch64 1.83.0-9.fc42        fedora                                                             67.7 KiB
 boost-date-time           aarch64 1.83.0-9.fc42        fedora                                                             67.3 KiB
 boost-fiber               aarch64 1.83.0-9.fc42        fedora                                                            131.8 KiB
 boost-filesystem          aarch64 1.83.0-9.fc42        fedora                                                            132.0 KiB
 boost-graph               aarch64 1.83.0-9.fc42        fedora                                                            324.2 KiB
 boost-iostreams           aarch64 1.83.0-9.fc42        fedora                                                            131.7 KiB
 boost-json                aarch64 1.83.0-9.fc42        fedora                                                            324.0 KiB
 boost-locale              aarch64 1.83.0-9.fc42        fedora                                                            580.4 KiB
 boost-log                 aarch64 1.83.0-9.fc42        fedora                                                              1.4 MiB
 boost-math                aarch64 1.83.0-9.fc42        fedora                                                            847.2 KiB
 boost-nowide              aarch64 1.83.0-9.fc42        fedora                                                             67.7 KiB
 boost-numpy3              aarch64 1.83.0-9.fc42        fedora                                                             67.7 KiB
 boost-program-options     aarch64 1.83.0-9.fc42        fedora                                                            259.7 KiB
 boost-python3             aarch64 1.83.0-9.fc42        fedora                                                            263.1 KiB
 boost-random              aarch64 1.83.0-9.fc42        fedora                                                             67.7 KiB
 boost-regex               aarch64 1.83.0-9.fc42        fedora                                                            259.7 KiB
 boost-serialization       aarch64 1.83.0-9.fc42        fedora                                                            454.1 KiB
 boost-stacktrace          aarch64 1.83.0-9.fc42        fedora                                                            200.0 KiB
 boost-system              aarch64 1.83.0-9.fc42        fedora                                                             67.3 KiB
 boost-test                aarch64 1.83.0-9.fc42        fedora                                                            646.6 KiB
 boost-thread              aarch64 1.83.0-9.fc42        fedora                                                            131.8 KiB
 boost-timer               aarch64 1.83.0-9.fc42        fedora                                                             67.7 KiB
 boost-type_erasure        aarch64 1.83.0-9.fc42        fedora                                                             67.7 KiB
 boost-wave                aarch64 1.83.0-9.fc42        fedora                                                            644.4 KiB
 cmake-data                noarch  3.31.2-1.fc42        copr_base                                                           8.5 MiB
 cmake-filesystem          aarch64 3.31.2-1.fc42        copr_base                                                           0.0   B
 cmake-rpm-macros          noarch  3.31.2-1.fc42        copr_base                                                           7.5 KiB
 cpp                       aarch64 15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch  35.3 MiB
 emacs-filesystem          noarch  1:30.0-3.fc41        fedora                                                              0.0   B
 expat                     aarch64 2.6.4-1.fc42         copr_base                                                         343.6 KiB
 flexiblas                 aarch64 3.4.4-3.fc42         copr_base                                                          48.5 KiB
 flexiblas-netlib          aarch64 3.4.4-3.fc42         copr_base                                                           9.1 MiB
 flexiblas-openblas-openmp aarch64 3.4.4-3.fc42         copr_base                                                          66.3 KiB
 gcc-plugin-annobin        aarch64 15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch  67.5 KiB
 glibc-devel               aarch64 2.40.9000-24.fc42    copr_base                                                           2.2 MiB
 gmock                     aarch64 1.14.0-5.fc42        copr_base                                                         197.9 KiB
 gtest                     aarch64 1.14.0-5.fc42        copr_base                                                         518.0 KiB
 jsoncpp                   aarch64 1.9.5-8.fc42         copr_base                                                         268.8 KiB
 kernel-headers            aarch64 6.13.0-0.rc3.29.fc42 fedora                                                              6.4 MiB
 libasan                   aarch64 15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch   1.5 MiB
 libatomic                 aarch64 15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch  66.1 KiB
 libb2                     aarch64 0.98.1-12.fc42       copr_base                                                          72.8 KiB
 libcutl                   aarch64 1.10.0-31.fc42       copr_base                                                           1.0 MiB
 libgfortran               aarch64 15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch   1.7 MiB
 libicu                    aarch64 76.1-1.fc42          copr_base                                                          36.5 MiB
 libicu-devel              aarch64 76.1-1.fc42          copr_base                                                           5.1 MiB
 libmpc                    aarch64 1.3.1-6.fc42         copr_base                                                         149.9 KiB
 libstdc++-devel           aarch64 15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch  15.4 MiB
 libubsan                  aarch64 15.0.0-0.2.fc42      https_fedorapeople_org_dmalcolm_gcc_gcc_15_mass_prebuild_basearch 460.6 KiB
 libuv                     aarch64 1:1.49.2-1.fc42      copr_base                                                         595.3 KiB
 libxcrypt-devel           aarch64 4.4.36-11.fc42       fedora                                                             30.5 KiB
 mpdecimal                 aarch64 2.5.1-16.fc42        copr_base                                                         259.9 KiB
 openblas                  aarch64 0.3.28-2.fc42        copr_base                                                         106.6 KiB
 openblas-openmp           aarch64 0.3.28-2.fc42        copr_base                                                          20.3 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                   aarch64 3.13.1-2.fc42        fedora                                                             82.5 KiB
 python3-libs              aarch64 3.13.1-2.fc42        fedora                                                             41.7 MiB
 python3-numpy             aarch64 1:2.2.0-3.fc42       fedora                                                             33.9 MiB
 python3-numpy-f2py        aarch64 1:2.2.0-3.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                     aarch64 1.4.5-1.fc42         fedora                                                            587.1 KiB
 sqlite                    aarch64 3.47.2-1.fc42        fedora                                                              1.8 MiB
 tokyocabinet              aarch64 1.4.48-26.fc41       fedora                                                              4.3 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                  aarch64 3.3.0-5.fc42         fedora                                                              3.6 MiB

Transaction Summary:
 Installing:        93 packages

Total size of inbound packages is 139 MiB. Need to download 139 MiB.
After this operation, 607 MiB extra will be used (install 607 MiB, remove 0 B).
[ 1/93] libtirpc-devel-0:1.3.6-1.fc42.a 100% |   7.2 MiB/s | 125.5 KiB |  00m00s
[ 2/93] sqlite-devel-0:3.47.2-1.fc42.aa 100% |  29.4 MiB/s | 150.3 KiB |  00m00s
[ 3/93] tokyocabinet-devel-0:1.4.48-26. 100% |  21.7 MiB/s |  88.8 KiB |  00m00s
[ 4/93] xerces-c-devel-0:3.3.0-5.fc42.a 100% | 125.3 MiB/s | 513.1 KiB |  00m00s
[ 5/93] python3-devel-0:3.13.1-2.fc42.a 100% | 131.2 MiB/s | 403.0 KiB |  00m00s
[ 6/93] boost-devel-0:1.83.0-9.fc42.aar 100% | 218.1 MiB/s |  14.2 MiB |  00m00s
[ 7/93] xsd-0:4.1.0-0.16.a11.fc42.aarch 100% |  34.5 MiB/s |   1.0 MiB |  00m00s
[ 8/93] zlib-ng-compat-devel-0:2.2.2-1. 100% |  18.6 MiB/s |  38.1 KiB |  00m00s
[ 9/93] bzip2-devel-0:1.0.8-19.fc42.aar 100% |  20.9 MiB/s | 214.2 KiB |  00m00s
[10/93] boost-static-0:1.83.0-9.fc42.aa 100% |  35.3 MiB/s |   3.4 MiB |  00m00s
[11/93] cmake-0:3.31.2-1.fc42.aarch64   100% | 197.3 MiB/s |   7.5 MiB |  00m00s
[12/93] gtest-devel-0:1.14.0-5.fc42.aar 100% |  79.0 MiB/s | 242.8 KiB |  00m00s
[13/93] make-1:4.4.1-9.fc42.aarch64     100% | 186.9 MiB/s | 574.2 KiB |  00m00s
[14/93] boost-0:1.83.0-9.fc42.aarch64   100% |  12.6 MiB/s |  12.9 KiB |  00m00s
[15/93] boost-numpy3-0:1.83.0-9.fc42.aa 100% |  25.1 MiB/s |  25.7 KiB |  00m00s
[16/93] sqlite-0:3.47.2-1.fc42.aarch64  100% | 166.2 MiB/s | 850.9 KiB |  00m00s
[17/93] tokyocabinet-0:1.4.48-26.fc41.a 100% | 100.9 MiB/s | 516.7 KiB |  00m00s
[18/93] xerces-c-0:3.3.0-5.fc42.aarch64 100% | 124.7 MiB/s | 893.8 KiB |  00m00s
[19/93] python3-0:3.13.1-2.fc42.aarch64 100% |  26.3 MiB/s |  26.9 KiB |  00m00s
[20/93] python3-libs-0:3.13.1-2.fc42.aa 100% | 275.8 MiB/s |   8.8 MiB |  00m00s
[21/93] rhash-0:1.4.5-1.fc42.aarch64    100% |  95.8 MiB/s | 196.2 KiB |  00m00s
[22/93] gcc-c++-0:15.0.0-0.2.fc42.aarch 100% |  49.6 MiB/s |  13.6 MiB |  00m00s
[23/93] libstdc++-devel-0:15.0.0-0.2.fc 100% |  82.6 MiB/s |   2.6 MiB |  00m00s
[24/93] gmock-0:1.14.0-5.fc42.aarch64   100% |  52.9 MiB/s |  54.1 KiB |  00m00s
[25/93] gtest-0:1.14.0-5.fc42.aarch64   100% |  51.6 MiB/s | 158.4 KiB |  00m00s
[26/93] boost-atomic-0:1.83.0-9.fc42.aa 100% |  16.5 MiB/s |  16.9 KiB |  00m00s
[27/93] boost-chrono-0:1.83.0-9.fc42.aa 100% |  22.0 MiB/s |  22.5 KiB |  00m00s
[28/93] boost-container-0:1.83.0-9.fc42 100% |  17.9 MiB/s |  36.6 KiB |  00m00s
[29/93] boost-context-0:1.83.0-9.fc42.a 100% |   7.2 MiB/s |  14.8 KiB |  00m00s
[30/93] boost-contract-0:1.83.0-9.fc42. 100% |  19.1 MiB/s |  39.1 KiB |  00m00s
[31/93] boost-coroutine-0:1.83.0-9.fc42 100% |  17.4 MiB/s |  17.9 KiB |  00m00s
[32/93] boost-date-time-0:1.83.0-9.fc42 100% |  13.3 MiB/s |  13.6 KiB |  00m00s
[33/93] boost-fiber-0:1.83.0-9.fc42.aar 100% |  37.3 MiB/s |  38.2 KiB |  00m00s
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[38/93] boost-locale-0:1.83.0-9.fc42.aa 100% |  91.2 MiB/s | 186.7 KiB |  00m00s
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[40/93] cpp-0:15.0.0-0.2.fc42.aarch64   100% |  40.7 MiB/s |  11.4 MiB |  00m00s
[41/93] boost-math-0:1.83.0-9.fc42.aarc 100% |  17.7 MiB/s | 254.2 KiB |  00m00s
[42/93] boost-nowide-0:1.83.0-9.fc42.aa 100% |  17.9 MiB/s |  18.4 KiB |  00m00s
[43/93] boost-program-options-0:1.83.0- 100% |  46.1 MiB/s |  94.4 KiB |  00m00s
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[51/93] boost-thread-0:1.83.0-9.fc42.aa 100% |  26.3 MiB/s |  53.9 KiB |  00m00s
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[54/93] boost-wave-0:1.83.0-9.fc42.aarc 100% |  45.7 MiB/s | 187.1 KiB |  00m00s
[55/93] python-pip-wheel-0:24.3.1-1.fc4 100% | 150.5 MiB/s |   1.2 MiB |  00m00s
[56/93] tzdata-0:2024b-1.fc42.noarch    100% |  99.4 MiB/s | 712.7 KiB |  00m00s
[57/93] libmpc-0:1.3.1-6.fc42.aarch64   100% |  34.2 MiB/s |  70.0 KiB |  00m00s
[58/93] glibc-devel-0:2.40.9000-24.fc42 100% |  91.4 MiB/s | 561.6 KiB |  00m00s
[59/93] kernel-headers-0:6.13.0-0.rc3.2 100% | 134.4 MiB/s |   1.6 MiB |  00m00s
[60/93] libxcrypt-devel-0:4.4.36-11.fc4 100% |   5.5 MiB/s |  28.1 KiB |  00m00s
[61/93] libatomic-0:15.0.0-0.2.fc42.aar 100% | 969.3 KiB/s |  17.4 KiB |  00m00s
[62/93] libasan-0:15.0.0-0.2.fc42.aarch 100% |  22.3 MiB/s | 456.3 KiB |  00m00s
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[66/93] libb2-0:0.98.1-12.fc42.aarch64  100% |  24.2 MiB/s |  24.8 KiB |  00m00s
[67/93] mpdecimal-0:2.5.1-16.fc42.aarch 100% |  42.4 MiB/s |  86.8 KiB |  00m00s
[68/93] libubsan-0:15.0.0-0.2.fc42.aarc 100% |   9.7 MiB/s | 188.3 KiB |  00m00s
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[70/93] gcc-0:15.0.0-0.2.fc42.aarch64   100% |  66.3 MiB/s |  35.1 MiB |  00m01s
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[72/93] libicu-0:76.1-1.fc42.aarch64    100% | 115.9 MiB/s |  10.5 MiB |  00m00s
[73/93] libicu-devel-0:76.1-1.fc42.aarc 100% |  43.2 MiB/s | 751.7 KiB |  00m00s
[74/93] emacs-filesystem-1:30.0-3.fc41. 100% |   3.5 MiB/s |   7.1 KiB |  00m00s
[75/93] vim-filesystem-2:9.1.919-1.fc42 100% |   8.0 MiB/s |  16.4 KiB |  00m00s
[76/93] cmake-data-0:3.31.2-1.fc42.noar 100% |  89.9 MiB/s |   1.9 MiB |  00m00s
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[78/93] libuv-1:1.49.2-1.fc42.aarch64   100% |  62.5 MiB/s | 256.1 KiB |  00m00s
[79/93] flexiblas-0:3.4.4-3.fc42.aarch6 100% |   8.4 MiB/s |  25.8 KiB |  00m00s
[80/93] flexiblas-openblas-openmp-0:3.4 100% |   2.6 MiB/s |  15.8 KiB |  00m00s
[81/93] flexiblas-netlib-0:3.4.4-3.fc42 100% | 119.2 MiB/s |   2.7 MiB |  00m00s
[82/93] openblas-openmp-0:0.3.28-2.fc42 100% | 158.6 MiB/s |   4.0 MiB |  00m00s
[83/93] openblas-0:0.3.28-2.fc42.aarch6 100% |   6.7 MiB/s |  41.4 KiB |  00m00s
[84/93] pyproject-rpm-macros-0:1.16.3-1 100% |  21.8 MiB/s |  44.6 KiB |  00m00s
[85/93] python-rpm-macros-0:3.13-3.fc41 100% |   8.6 MiB/s |  17.7 KiB |  00m00s
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[88/93] libgfortran-0:15.0.0-0.2.fc42.a 100% |  14.3 MiB/s | 440.5 KiB |  00m00s
[89/93] python3-packaging-0:24.2-2.fc42 100% |  75.1 MiB/s | 153.8 KiB |  00m00s
[90/93] annobin-plugin-gcc-0:12.79-1.fc 100% | 119.2 MiB/s | 976.3 KiB |  00m00s
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[93/93] annobin-docs-0:12.79-1.fc42.noa 100% |  45.5 MiB/s |  93.2 KiB |  00m00s
--------------------------------------------------------------------------------
[93/93] Total                           100% | 173.0 MiB/s | 139.4 MiB |  00m01s
Running transaction
[ 1/95] Verify package files            100% | 184.0   B/s |  93.0   B |  00m01s
[ 2/95] Prepare transaction             100% | 494.0   B/s |  93.0   B |  00m00s
[ 3/95] Installing boost-system-0:1.83. 100% |  66.7 MiB/s |  68.3 KiB |  00m00s
[ 4/95] Installing boost-chrono-0:1.83. 100% |  67.1 MiB/s |  68.7 KiB |  00m00s
[ 5/95] Installing boost-thread-0:1.83. 100% | 129.7 MiB/s | 132.8 KiB |  00m00s
[ 6/95] Installing libicu-0:76.1-1.fc42 100% | 347.5 MiB/s |  36.5 MiB |  00m00s
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[10/95] Installing expat-0:2.6.4-1.fc42 100% | 168.8 MiB/s | 345.6 KiB |  00m00s
[11/95] Installing libmpc-0:1.3.1-6.fc4 100% | 147.9 MiB/s | 151.5 KiB |  00m00s
[12/95] Installing boost-context-0:1.83 100% |  66.8 MiB/s |  68.4 KiB |  00m00s
[13/95] Installing boost-atomic-0:1.83. 100% |  67.0 MiB/s |  68.6 KiB |  00m00s
[14/95] Installing boost-filesystem-0:1 100% | 129.9 MiB/s | 133.0 KiB |  00m00s
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[16/95] Installing libgfortran-0:15.0.0 100% | 338.2 MiB/s |   1.7 MiB |  00m00s
[17/95] Installing boost-date-time-0:1. 100% |  66.7 MiB/s |  68.3 KiB |  00m00s
[18/95] Installing boost-container-0:1. 100% |  67.1 MiB/s |  68.7 KiB |  00m00s
[19/95] Installing gtest-0:1.14.0-5.fc4 100% | 253.6 MiB/s | 519.4 KiB |  00m00s
[20/95] Installing xerces-c-0:3.3.0-5.f 100% | 401.0 MiB/s |   3.6 MiB |  00m00s
[21/95] Installing make-1:4.4.1-9.fc42. 100% | 263.7 MiB/s |   1.8 MiB |  00m00s
[22/95] Installing gmock-0:1.14.0-5.fc4 100% | 194.7 MiB/s | 199.4 KiB |  00m00s
[23/95] Installing boost-json-0:1.83.0- 100% | 317.4 MiB/s | 325.0 KiB |  00m00s
[24/95] Installing boost-wave-0:1.83.0- 100% | 315.1 MiB/s | 645.4 KiB |  00m00s
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[26/95] Installing boost-fiber-0:1.83.0 100% | 129.7 MiB/s | 132.8 KiB |  00m00s
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[28/95] Installing boost-coroutine-0:1. 100% |  67.1 MiB/s |  68.7 KiB |  00m00s
[29/95] Installing cpp-0:15.0.0-0.2.fc4 100% | 330.0 MiB/s |  35.3 MiB |  00m00s
[30/95] Installing libcutl-0:1.10.0-31. 100% | 251.9 MiB/s |   1.0 MiB |  00m00s
[31/95] Installing boost-graph-0:1.83.0 100% | 158.8 MiB/s | 325.2 KiB |  00m00s
[32/95] Installing boost-locale-0:1.83. 100% | 189.3 MiB/s | 581.4 KiB |  00m00s
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[34/95] Installing boost-type_erasure-0 100% |  67.1 MiB/s |  68.7 KiB |  00m00s
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[36/95] Installing annobin-docs-0:12.79 100% |  97.4 MiB/s |  99.7 KiB |  00m00s
[37/95] Installing openblas-0:0.3.28-2. 100% | 105.8 MiB/s | 108.3 KiB |  00m00s
[38/95] Installing openblas-openmp-0:0. 100% | 432.3 MiB/s |  20.3 MiB |  00m00s
[39/95] Installing flexiblas-0:3.4.4-3. 100% |  48.5 MiB/s |  49.7 KiB |  00m00s
[40/95] Installing flexiblas-openblas-o 100% |  65.6 MiB/s |  67.2 KiB |  00m00s
[41/95] Installing flexiblas-netlib-0:3 100% | 324.4 MiB/s |   9.1 MiB |  00m00s
[42/95] Installing libuv-1:1.49.2-1.fc4 100% | 194.7 MiB/s | 598.1 KiB |  00m00s
[43/95] Installing jsoncpp-0:1.9.5-8.fc 100% | 132.0 MiB/s | 270.3 KiB |  00m00s
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[46/95] Installing mpdecimal-0:2.5.1-16 100% | 254.9 MiB/s | 261.0 KiB |  00m00s
[47/95] Installing libb2-0:0.98.1-12.fc 100% |  72.1 MiB/s |  73.9 KiB |  00m00s
[48/95] Installing libubsan-0:15.0.0-0. 100% | 225.3 MiB/s | 461.4 KiB |  00m00s
[49/95] Installing libatomic-0:15.0.0-0 100% |   0.0   B/s |  66.9 KiB |  00m00s
[50/95] Installing libasan-0:15.0.0-0.2 100% | 216.1 MiB/s |   1.5 MiB |  00m00s
[51/95] Installing kernel-headers-0:6.1 100% | 159.3 MiB/s |   6.5 MiB |  00m00s
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[53/95] Installing glibc-devel-0:2.40.9 100% | 120.4 MiB/s |   2.3 MiB |  00m00s
[54/95] Installing gcc-0:15.0.0-0.2.fc4 100% | 350.6 MiB/s |  97.8 MiB |  00m00s
[55/95] Installing tzdata-0:2024b-1.fc4 100% |  40.1 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% | 271.6 MiB/s |  42.1 MiB |  00m00s
[58/95] Installing python3-0:3.13.1-2.f 100% |  82.3 MiB/s |  84.3 KiB |  00m00s
[59/95] Installing boost-python3-0:1.83 100% | 128.9 MiB/s | 264.1 KiB |  00m00s
[60/95] Installing cmake-rpm-macros-0:3 100% |   8.0 MiB/s |   8.2 KiB |  00m00s
[61/95] Installing python3-packaging-0: 100% | 138.7 MiB/s | 568.0 KiB |  00m00s
[62/95] Installing python3-rpm-generato 100% |  81.0 MiB/s |  82.9 KiB |  00m00s
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[65/95] Installing python3-numpy-f2py-1 100% | 129.2 MiB/s |   2.1 MiB |  00m00s
[66/95] Installing boost-numpy3-0:1.83. 100% |  67.0 MiB/s |  68.7 KiB |  00m00s
[67/95] Installing boost-test-0:1.83.0- 100% | 210.9 MiB/s | 648.0 KiB |  00m00s
[68/95] Installing boost-stacktrace-0:1 100% | 197.1 MiB/s | 201.8 KiB |  00m00s
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[71/95] Installing boost-program-option 100% | 254.6 MiB/s | 260.7 KiB |  00m00s
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[75/95] Installing boost-contract-0:1.8 100% | 129.7 MiB/s | 132.8 KiB |  00m00s
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[82/95] Installing tokyocabinet-0:1.4.4 100% | 396.1 MiB/s |   4.4 MiB |  00m00s
[83/95] Installing sqlite-0:3.47.2-1.fc 100% | 253.4 MiB/s |   1.8 MiB |  00m00s
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[87/95] Installing boost-static-0:1.83. 100% | 533.8 MiB/s |  36.8 MiB |  00m00s
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[90/95] Installing xsd-0:4.1.0-0.16.a11 100% | 234.4 MiB/s |   4.7 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% | 200.5 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% |   1.4 MiB/s | 263.1 KiB |  00m00s
Warning: skipped OpenPGP checks for 35 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: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1729209600
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.akktBH
+ 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.UVzhpd
+ 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.PVEvc4
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,pack-relative-relocs -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
+ mkdir -p percolator
+ pushd 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
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,pack-relative-relocs -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -Wl,-z,pack-relative-relocs -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=aarch64 ..
-- 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 = aarch64
-- 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 (1.7s)
-- 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 -j4 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
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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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make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 19%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o -c /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/picked_protein/PeptideSrc.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'
[ 12%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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]: 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'
[  3%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[  1%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_in.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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o -MF CMakeFiles/perclibrary.dir/percolator_in.cxx.o.d -o CMakeFiles/perclibrary.dir/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/percolator_in.cxx
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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);
      |         ^
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
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/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++)
      |                 ~^~~~~~~~~~~
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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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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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[ 30%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -MF CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o.d -o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o -c /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/picked_protein/ProteinPeptideIterator.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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -MF CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o.d -o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o -c /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/picked_protein/PickedProteinCaller.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/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/cmake -E cmake_link_script CMakeFiles/picked_protein.dir/link.txt --verbose=1
/usr/bin/ar qc libpicked_protein.a CMakeFiles/picked_protein.dir/__/Globals.cpp.o CMakeFiles/picked_protein.dir/__/Logger.cpp.o CMakeFiles/picked_protein.dir/__/MyException.cpp.o CMakeFiles/picked_protein.dir/__/Option.cpp.o CMakeFiles/picked_protein.dir/Database.cpp.o CMakeFiles/picked_protein.dir/Peptide.cpp.o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o CMakeFiles/picked_protein.dir/Protein.cpp.o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
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[ 33%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
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[ 34%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 23%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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/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/percolator'
[ 31%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 36%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 38%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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/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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 41%] 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'
[ 41%] 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'
[ 43%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 40%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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) :
      |   ^~~~~~~~~~~
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/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'
[ 44%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 39%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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) {
      |                 ~~~~^~~~~~~~~~~
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/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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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]: 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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]: 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'
[ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 45%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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]: 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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]: 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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]: 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 {
      |               ^~~~~~~~
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'
[ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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 {
      |               ^~~~~~~~
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'
[ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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 {
      |               ^~~~~~~~
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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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]: 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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]: 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 79%] Building CXX object src/CMakeFiles/perclibrary.dir/Timer.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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/Timer.cpp.o -MF CMakeFiles/perclibrary.dir/Timer.cpp.o.d -o CMakeFiles/perclibrary.dir/Timer.cpp.o -c /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/Timer.cpp
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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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/GoogleAnalytics.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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT src/CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o -MF CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o.d -o CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o -c /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/GoogleAnalytics.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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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 {
      |               ^~~~~~~~
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()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 82%] Linking CXX static library libperclibrary.a
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary.dir/link.txt --verbose=1
/usr/bin/ar qc libperclibrary.a CMakeFiles/perclibrary.dir/percolator_in.cxx.o CMakeFiles/perclibrary.dir/percolator_out.cxx.o CMakeFiles/perclibrary.dir/parser.cxx.o CMakeFiles/perclibrary.dir/serializer.cxx.o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o CMakeFiles/perclibrary.dir/SetHandler.cpp.o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o CMakeFiles/perclibrary.dir/svm.cpp.o CMakeFiles/perclibrary.dir/Caller.cpp.o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o CMakeFiles/perclibrary.dir/Enzyme.cpp.o CMakeFiles/perclibrary.dir/Globals.cpp.o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o CMakeFiles/perclibrary.dir/Normalizer.cpp.o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o CMakeFiles/perclibrary.dir/DataSet.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Option.cpp.o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o CMakeFiles/perclibrary.dir/ssl.cpp.o CMakeFiles/perclibrary.dir/PackedVector.cpp.o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o CMakeFiles/perclibrary.dir/Matrix.cpp.o CMakeFiles/perclibrary.dir/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/FidoInterface.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o CMakeFiles/perclibrary.dir/Timer.cpp.o CMakeFiles/perclibrary.dir/TmpDir.cpp.o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
/usr/bin/ranlib libperclibrary.a
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/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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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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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 src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/build
/usr/bin/make  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build
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[ 86%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 88%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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_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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 87%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 89%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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]: 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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]: 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'
[ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 90%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,pack-relative-relocs -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,pack-relative-relocs -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
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'
[ 98%] Built target qvality
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'
[ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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]: 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,pack-relative-relocs -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,pack-relative-relocs -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'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/percolator'
[ 93%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,pack-relative-relocs -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,pack-relative-relocs -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'
/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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,pack-relative-relocs -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -Wl,-z,pack-relative-relocs -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=aarch64 ../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 (0.8s)
-- 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 -j4 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'
[ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
/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]: 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'
[ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
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]: 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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/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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido'
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:
../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:
/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-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/fido'
[ 25%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido'
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:
../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:
/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 ‘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'
[ 37%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/fido'
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
      |            ^~~~~~~~~~~~~~~
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: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]: 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,pack-relative-relocs -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc' '-DCMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=-Wl,-z,relro   -Wl,-z,pack-relative-relocs -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=aarch64 ../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 = aarch64
-- 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 (2.0s)
-- 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 -j4 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
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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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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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[  7%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
make[2]: Leaving directory '/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/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));
      |            ^
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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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make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
[ 19%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/LazyMatrix.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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o -MF CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o.d -o CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o -c /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.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/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 â€make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
˜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++ ) {
      |                                                                          ~~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
[ 21%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -MF CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o.d -o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o -c /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/MSConvertFile.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'
[ 23%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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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[ 25%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
make[2]: Leaving directory '/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/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]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
[ 26%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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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[ 28%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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;
      |                      ^~
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/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 -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o -MF CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o.d -o CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o -c /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/percolator_in.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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[ 30%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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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[ 33%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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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[ 35%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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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/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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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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o -MF CMakeFiles/MSToolkit.dir/crawutils.cpp.o.d -o CMakeFiles/MSToolkit.dir/crawutils.cpp.o -c /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-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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[ 44%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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_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:1266:23: 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'
[ 62%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 17%] Building CXX object CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o -MF CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o.d -o CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o -c /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/mzIdentML1.1.0.cxx
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'
[ 64%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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[](unsignemake[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
d 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'
[ 58%] Building CXX object CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -MF CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o.d -o CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o -c /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters/tandem2011.12.01.1.cxx
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'
[ 66%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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[] = {
      |                     ^~~~~~~~~~~~
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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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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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/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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/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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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
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/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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/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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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;
      |            ^~~~~~~~~~
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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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/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);
      |                      ~~~~~~~^~~~
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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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make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
[ 92%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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'
[ 91%] Building CXX object CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -std=gnu++11 -MD -MT CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -MF CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o.d -o CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -c /builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/src/converters/Msgfplus2Pin.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 sqt2pin
/usr/bin/cmake -E cmake_link_script CMakeFiles/sqt2pin.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,pack-relative-relocs -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,pack-relative-relocs -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/sqt2pin.dir/link.d CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -o sqt2pin   -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 sqt2pin
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'
[ 98%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,pack-relative-relocs -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,pack-relative-relocs -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
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[2]: Leaving directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
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'
make[2]: Entering directory '/builddir/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/converters'
[100%] 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I../src -I/usr/include/xsd/cxx/tree -I/usr/include/tirpc -O3 -DNDEBUG -Wl,-z,relro   -Wl,-z,pack-relative-relocs -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,pack-relative-relocs -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'
/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.EbOVk6
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,pack-relative-relocs -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 -j4 --strict-build-id -m -i --build-id-seed 3.06.04-5.fc42 --unique-debug-suffix -3.06.04-5.fc42.aarch64 --unique-debug-src-base percolator-3.06.04-5.fc42.aarch64 --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.aarch64
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 -j4
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-determinism --brp -j4 /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/libRAMP.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/libMSToolkit.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/libperclibrary.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.wnv32y
+ 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  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro   -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd percolator-rel-3-06-04
+ mkdir -p test
+ pushd test
~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04/test ~/build/BUILD/percolator-3.06.04-build/percolator-rel-3-06-04
+ ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt

Pin-converter version 3.06.4, Build Date 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 84ab1b4596124a208713b1214a0b9be8
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 Sat Dec 21 00:11:45 2024
 on 84ab1b4596124a208713b1214a0b9be8
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 0.4802 cpu seconds or 0 seconds wall clock time.
---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
Iteration 1:	Estimated 10193 PSMs with q<0.01
Iteration 2:	Estimated 11236 PSMs with q<0.01
Iteration 3:	Estimated 11461 PSMs with q<0.01
Iteration 4:	Estimated 11509 PSMs with q<0.01
Iteration 5:	Estimated 11560 PSMs with q<0.01
Iteration 6:	Estimated 11576 PSMs with q<0.01
Iteration 7:	Estimated 11602 PSMs with q<0.01
Iteration 8:	Estimated 11617 PSMs with q<0.01
Iteration 9:	Estimated 11617 PSMs with q<0.01
Iteration 10:	Estimated 11616 PSMs with q<0.01
Learned normalized SVM weights for the 3 cross-validation splits:
 Split1	 Split2	 Split3	FeatureName
-0.4835	-0.3200	-0.4134	lnrSp
 0.1414	 0.1989	 0.1695	deltLCn
 0.6622	 0.6394	 0.7524	deltCn
 0.6588	 0.6486	 0.6804	Xcorr
-0.0413	 0.0625	-0.0978	Sp
 0.0244	 0.1588	 0.2191	IonFrac
 0.8867	 0.6292	 0.4141	Mass
-0.7489	-0.3031	-0.0249	PepLen
 0.1083	 0.1800	 0.1009	Charge1
 0.0250	 0.0242	 0.0043	Charge2
-0.0471	-0.0610	-0.0250	Charge3
 1.3220	 1.2346	 1.2522	enzN
 1.3377	 1.1510	 1.1172	enzC
-1.9073	-1.7718	-1.6438	enzInt
-0.0159	-0.0088	 0.1201	lnNumSP
 0.0188	 0.0011	 0.0218	dM
 0.0044	 0.0139	 0.0016	absdM
-6.5792	-6.3779	-5.8394	m0
Found 11446 test set PSMs with q<0.01.
Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide.
Selecting pi_0=0.86749
Calculating q values.
New pi_0 estimate on final list yields 7371 target peptides with q<0.01.
Calculating posterior error probabilities (PEPs).
Processing took 20.7659 cpu seconds or 10 seconds wall clock time.
+ popd
~/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
+ pushd percolator
+ /usr/bin/ctest --test-dir . --output-on-failure --force-new-ctest-process -j4
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    0.02 sec

100% tests passed, 0 tests failed out of 1

Total Test time (real) =   0.02 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.aarch64
Provides: percolator = 3.06.04-5.fc42 percolator(aarch-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: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.25)(64bit) libc.so.6(GLIBC_2.28)(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_ABI_DT_RELR)(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_2.17)(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.Ah47vX
+ 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.Ugn9Xb
+ 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.aarch64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.3Po8Ft
+ 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.DBX3AQ
+ 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(aarch-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.aarch64
Provides: percolator-debugsource = 3.06.04-5.fc42 percolator-debugsource(aarch-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.aarch64
Provides: debuginfo(build-id) = 0279cc4d2cd242b95f5352d9f076c386f295fe96 debuginfo(build-id) = 136def67a8e17a9d2b9e5ca37763cc045d778dd7 debuginfo(build-id) = 1aa9cc58f21c88eb2ea0cb3b9feec6a67156e91e debuginfo(build-id) = 91b51684260c02efd92daaf6124aac60a6af77e6 debuginfo(build-id) = f710ecaedc11096a78e141e18449b81a5d3800af percolator-debuginfo = 3.06.04-5.fc42 percolator-debuginfo(aarch-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(aarch-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-debugsource-3.06.04-5.fc42.aarch64.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.06.04-5.fc42.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-3.06.04-5.fc42.aarch64.rpm
Wrote: /builddir/build/RPMS/percolator-static-3.06.04-5.fc42.aarch64.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.06.04-5.fc42.aarch64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.l0gcMt
+ 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-aarch64-1734739672.320230/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) 3 minutes 58 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": "aarch64"
        },
        {
            "name": "percolator-data",
            "epoch": null,
            "version": "3.06.04",
            "release": "5.fc42",
            "arch": "noarch"
        },
        {
            "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": "aarch64"
        },
        {
            "name": "percolator-debuginfo",
            "epoch": null,
            "version": "3.06.04",
            "release": "5.fc42",
            "arch": "aarch64"
        },
        {
            "name": "percolator-debugsource",
            "epoch": null,
            "version": "3.06.04",
            "release": "5.fc42",
            "arch": "aarch64"
        }
    ]
}
RPMResults finished