Warning: Permanently added '54.210.112.183' (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/6951371-fedora-rawhide-aarch64 --chroot fedora-rawhide-aarch64


Version: 0.70
PID: 6118
Logging PID: 6119
Task:
{'appstream': False,
 'background': True,
 'build_id': 6951371,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-aarch64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '459667f54114258382b26a28cd3991104da93c93',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/percolator',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'percolator',
 'package_version': '3.06.04-3',
 'project_dirname': 'openblas-0.3.23',
 'project_name': 'openblas-0.3.23',
 'project_owner': 'psimovec',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/psimovec/openblas-0.3.23/fedora-rawhide-aarch64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None},
           {'baseurl': 'http://kojipkgs.fedoraproject.org/repos/rawhide/latest/$basearch/',
            'id': 'http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch',
            'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch'}],
 'sandbox': 'psimovec/openblas-0.3.23--https://src.fedoraproject.org/user/releng',
 'source_json': {},
 'source_type': None,
 'submitter': 'https://src.fedoraproject.org/user/releng',
 'tags': [],
 'task_id': '6951371-fedora-rawhide-aarch64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/percolator /var/lib/copr-rpmbuild/workspace/workdir-kgpy6osc/percolator --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/percolator', '/var/lib/copr-rpmbuild/workspace/workdir-kgpy6osc/percolator', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-kgpy6osc/percolator'...

Running: git checkout 459667f54114258382b26a28cd3991104da93c93 --

cmd: ['git', 'checkout', '459667f54114258382b26a28cd3991104da93c93', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-kgpy6osc/percolator
rc: 0
stdout: 
stderr: Note: switching to '459667f54114258382b26a28cd3991104da93c93'.

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 459667f automatic import of percolator

Running: copr-distgit-client sources

cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-kgpy6osc/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/psimovec/openblas-0.3.23/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
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
100 5157k  100 5157k    0     0  47.5M      0 --:--:-- --:--:-- --:--:-- 47.9M
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/psimovec/openblas-0.3.23/percolator/yeast-01.sqt.tar.gz/md5/81e1997e1c1c193cbfcd4eb54c706af9/yeast-01.sqt.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 47.9M  100 47.9M    0     0  62.4M      0 --:--:-- --:--:-- --:--:-- 62.4M
INFO: Reading stdout from command: md5sum yeast-01.sqt.tar.gz

Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-kgpy6osc/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-kgpy6osc/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1706189148.512818 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.4 starting (python version = 3.11.3, NVR = mock-5.4-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-kgpy6osc/percolator/percolator.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-kgpy6osc/percolator --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1706189148.512818 -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-kgpy6osc/percolator/percolator.spec)  Config(fedora-rawhide-aarch64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.4
INFO: Mock Version: 5.4
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1706189148.512818/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide
INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide
INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1706189148.512818/root
INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture
INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount
INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/578de8690db86eae66e42ca97d0399a4a70d183fb6c2310eaec790247cd088b1/merged
INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/578de8690db86eae66e42ca97d0399a4a70d183fb6c2310eaec790247cd088b1/merged) with podman image umount
INFO: Using 'dnf' instead of 'dnf5' for bootstrap chroot
INFO: Package manager dnf detected and used (fallback)
INFO: Bootstrap image not marked ready
Start(bootstrap): installing dnf5 tooling
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  85 MB/s |  23 MB     00:00    
Additional repo http_kojipkgs_fedoraproject_org 214 MB/s |  73 MB     00:00    
fedora                                           49 MB/s |  70 MB     00:01    
Last metadata expiration check: 0:00:04 ago on Thu Jan 25 13:26:16 2024.
Dependencies resolved.
===========================================================================================================
 Package        Arch     Version       Repository                                                      Size
===========================================================================================================
Installing:
 dnf5           aarch64  5.1.11-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  509 k
 dnf5-plugins   aarch64  5.1.11-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  307 k
Installing dependencies:
 fmt            aarch64  10.2.1-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  121 k
 libdnf5        aarch64  5.1.11-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  849 k
 libdnf5-cli    aarch64  5.1.11-1.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  208 k
 sdbus-cpp      aarch64  1.4.0-1.fc40  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  102 k

Transaction Summary
===========================================================================================================
Install  6 Packages

Total download size: 2.0 M
Installed size: 6.7 M
Downloading Packages:
(1/6): dnf5-5.1.11-1.fc40.aarch64.rpm           8.4 MB/s | 509 kB     00:00    
(2/6): fmt-10.2.1-1.fc40.aarch64.rpm            1.9 MB/s | 121 kB     00:00    
(3/6): dnf5-plugins-5.1.11-1.fc40.aarch64.rpm   4.7 MB/s | 307 kB     00:00    
(4/6): libdnf5-5.1.11-1.fc40.aarch64.rpm         97 MB/s | 849 kB     00:00    
(5/6): sdbus-cpp-1.4.0-1.fc40.aarch64.rpm        15 MB/s | 102 kB     00:00    
(6/6): libdnf5-cli-5.1.11-1.fc40.aarch64.rpm     16 MB/s | 208 kB     00:00    
--------------------------------------------------------------------------------
Total                                            26 MB/s | 2.0 MB     00:00     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
  Installing       : fmt-10.2.1-1.fc40.aarch64                              1/6 
  Installing       : libdnf5-5.1.11-1.fc40.aarch64                          2/6 
  Installing       : libdnf5-cli-5.1.11-1.fc40.aarch64                      3/6 
  Installing       : dnf5-5.1.11-1.fc40.aarch64                             4/6 
  Installing       : sdbus-cpp-1.4.0-1.fc40.aarch64                         5/6 
  Installing       : dnf5-plugins-5.1.11-1.fc40.aarch64                     6/6 
  Running scriptlet: dnf5-plugins-5.1.11-1.fc40.aarch64                     6/6 

Installed:
  dnf5-5.1.11-1.fc40.aarch64             dnf5-plugins-5.1.11-1.fc40.aarch64     
  fmt-10.2.1-1.fc40.aarch64              libdnf5-5.1.11-1.fc40.aarch64          
  libdnf5-cli-5.1.11-1.fc40.aarch64      sdbus-cpp-1.4.0-1.fc40.aarch64         

Complete!
INFO: Switching package manager from dnf to the dnf5 (direct choice)
Finish(bootstrap): installing dnf5 tooling
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-1706189148.512818/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-4.19.1-2.fc40.aarch64
  rpm-sequoia-1.5.0-2.fc40.aarch64
  python3-dnf-4.18.2-1.fc40.noarch
  yum-4.18.2-1.fc40.noarch
  dnf5-5.1.11-1.fc40.aarch64
  dnf5-plugins-5.1.11-1.fc40.aarch64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 fedora                                 100% |  17.9 MiB/s |  19.7 MiB |  00m01s
>>> Downloading successful, but checksum doesn't match. Calculated: 190ef551af46
 Copr repository                        100% |  45.8 MiB/s |   4.0 MiB |  00m00s
 Additional repo http_kojipkgs_fedorapr 100% | 103.0 MiB/s |  17.1 MiB |  00m00s
Repositories loaded.
Package                           Arch    Version                    Repository                                                         Size
Installing group/module packages:                                                                                                           
 bash                             aarch64 5.2.26-1.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   8.3 MiB
 bzip2                            aarch64 1.0.8-16.fc39              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 427.5 KiB
 coreutils                        aarch64 9.4-3.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  20.7 MiB
 cpio                             aarch64 2.15-1.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.2 MiB
 diffutils                        aarch64 3.10-3.fc39                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.1 MiB
 fedora-release-common            noarch  40-0.29                    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  19.1 KiB
 findutils                        aarch64 1:4.9.0-6.fc40             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.7 MiB
 gawk                             aarch64 5.3.0-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   4.2 MiB
 glibc-minimal-langpack           aarch64 2.38.9000-33.fc40          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   0.0   B
 grep                             aarch64 3.11-5.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 gzip                             aarch64 1.12-6.fc39                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 475.8 KiB
 info                             aarch64 7.1-1.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 613.5 KiB
 patch                            aarch64 2.7.6-22.fc39              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 326.5 KiB
 redhat-rpm-config                noarch  280-1.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 183.2 KiB
 rpm-build                        aarch64 4.19.1-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.2 MiB
 sed                              aarch64 4.8-14.fc39                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 941.8 KiB
 shadow-utils                     aarch64 2:4.14.0-2.fc40            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   7.1 MiB
 tar                              aarch64 2:1.35-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   3.1 MiB
 unzip                            aarch64 6.0-62.fc39                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 726.6 KiB
 util-linux                       aarch64 2.39.3-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  16.5 MiB
 which                            aarch64 2.21-40.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 248.1 KiB
 xz                               aarch64 5.4.5-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.3 MiB
Installing dependencies:                                                                                                                    
 alternatives                     aarch64 1.26-1.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 218.2 KiB
 ansible-srpm-macros              noarch  1-12.fc40                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  35.7 KiB
 audit-libs                       aarch64 4.0-5.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 547.2 KiB
 authselect                       aarch64 1.5.0-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 312.4 KiB
 authselect-libs                  aarch64 1.5.0-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 basesystem                       noarch  11-18.fc39                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   0.0   B
 binutils                         aarch64 2.41-30.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  32.8 MiB
 binutils-gold                    aarch64 2.41-30.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   3.1 MiB
 bzip2-libs                       aarch64 1.0.8-16.fc39              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 200.7 KiB
 ca-certificates                  noarch  2023.2.62_v7.0.401-4.fc40  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.3 MiB
 coreutils-common                 aarch64 9.4-3.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  11.4 MiB
 cracklib                         aarch64 2.9.11-2.fc39              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 934.7 KiB
 crypto-policies                  noarch  20231204-1.git1e3a2e4.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 149.3 KiB
 curl                             aarch64 8.5.0-2.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 922.3 KiB
 cyrus-sasl-lib                   aarch64 2.1.28-17.fc40             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   3.1 MiB
 debugedit                        aarch64 5.0-12.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 498.8 KiB
 dwz                              aarch64 0.15-3.fc39                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 386.7 KiB
 ed                               aarch64 1.20-1.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 282.3 KiB
 efi-srpm-macros                  noarch  5-9.fc39                   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  40.1 KiB
 elfutils                         aarch64 0.190-4.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   5.0 MiB
 elfutils-debuginfod-client       aarch64 0.190-4.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 396.8 KiB
 elfutils-default-yama-scope      noarch  0.190-4.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.8 KiB
 elfutils-libelf                  aarch64 0.190-4.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 elfutils-libs                    aarch64 0.190-4.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.0 MiB
 fedora-gpg-keys                  noarch  40-0.2                     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 123.2 KiB
 fedora-release                   noarch  40-0.29                    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   0.0   B
 fedora-release-identity-basic    noarch  40-0.29                    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 694.0   B
 fedora-repos                     noarch  40-0.2                     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   4.9 KiB
 fedora-repos-rawhide             noarch  40-0.2                     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.2 KiB
 file                             aarch64 5.45-1.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 267.4 KiB
 file-libs                        aarch64 5.45-1.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  10.0 MiB
 filesystem                       aarch64 3.18-6.fc39                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 106.0   B
 fonts-srpm-macros                noarch  1:2.0.5-12.fc39            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  55.3 KiB
 forge-srpm-macros                noarch  0.2.0-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  37.4 KiB
 fpc-srpm-macros                  noarch  1.3-8.fc39                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 144.0   B
 gdb-minimal                      aarch64 14.1-6.fc40                copr_base                                                      12.1 MiB
 gdbm                             aarch64 1:1.23-4.fc39              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 928.3 KiB
 gdbm-libs                        aarch64 1:1.23-4.fc39              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 425.8 KiB
 ghc-srpm-macros                  noarch  1.6.1-3.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 369.0   B
 glibc                            aarch64 2.38.9000-33.fc40          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   9.7 MiB
 glibc-common                     aarch64 2.38.9000-33.fc40          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.6 MiB
 glibc-gconv-extra                aarch64 2.38.9000-33.fc40          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  49.0 MiB
 gmp                              aarch64 1:6.2.1-5.fc39             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 721.3 KiB
 gnat-srpm-macros                 noarch  6-3.fc39                   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.0 KiB
 go-srpm-macros                   noarch  3.3.1-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  60.6 KiB
 jansson                          aarch64 2.13.1-7.fc39              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 220.4 KiB
 kernel-srpm-macros               noarch  1.0-20.fc39                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.9 KiB
 keyutils-libs                    aarch64 1.6.3-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 226.3 KiB
 krb5-libs                        aarch64 1.21.2-3.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   3.4 MiB
 libacl                           aarch64 2.3.2-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 196.0 KiB
 libarchive                       aarch64 3.7.2-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.0 MiB
 libattr                          aarch64 2.5.2-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 196.5 KiB
 libblkid                         aarch64 2.39.3-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 392.9 KiB
 libbrotli                        aarch64 1.1.0-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 libcap                           aarch64 2.69-1.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.4 MiB
 libcap-ng                        aarch64 0.8.4-2.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 417.0 KiB
 libcom_err                       aarch64 1.47.0-2.fc39              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 239.2 KiB
 libcurl                          aarch64 8.5.0-2.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 856.5 KiB
 libeconf                         aarch64 0.5.2-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 204.0 KiB
 libevent                         aarch64 2.1.12-9.fc39              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.5 MiB
 libfdisk                         aarch64 2.39.3-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 494.9 KiB
 libffi                           aarch64 3.4.4-5.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 281.4 KiB
 libgcc                           aarch64 14.0.1-0.2.fc40            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 350.1 KiB
 libgomp                          aarch64 14.0.1-0.2.fc40            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 563.5 KiB
 libidn2                          aarch64 2.3.4-3.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 451.0 KiB
 libmount                         aarch64 2.39.3-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 484.2 KiB
 libnghttp2                       aarch64 1.59.0-1.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 262.1 KiB
 libnsl2                          aarch64 2.0.0-6.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 221.9 KiB
 libpkgconf                       aarch64 1.9.5-2.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 198.0 KiB
 libpsl                           aarch64 0.21.5-1.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 196.5 KiB
 libpwquality                     aarch64 1.4.5-6.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 libselinux                       aarch64 3.6-2.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 265.0 KiB
 libsemanage                      aarch64 3.6-1.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 361.4 KiB
 libsepol                         aarch64 3.6-1.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 874.1 KiB
 libsmartcols                     aarch64 2.39.3-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 288.1 KiB
 libssh                           aarch64 0.10.6-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 581.2 KiB
 libssh-config                    noarch  0.10.6-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 277.0   B
 libstdc++                        aarch64 14.0.1-0.2.fc40            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.8 MiB
 libtasn1                         aarch64 4.19.0-3.fc39              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 283.7 KiB
 libtirpc                         aarch64 1.3.4-1.rc1.fc40           http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 274.7 KiB
 libunistring                     aarch64 1.1-5.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.9 MiB
 libutempter                      aarch64 1.2.1-10.fc39              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 417.6 KiB
 libuuid                          aarch64 2.39.3-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 197.5 KiB
 libverto                         aarch64 0.3.2-6.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 197.4 KiB
 libxcrypt                        aarch64 4.4.36-4.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 398.9 KiB
 libxml2                          aarch64 2.12.4-1.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.2 MiB
 libzstd                          aarch64 1.5.5-4.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 795.9 KiB
 lua-libs                         aarch64 5.4.6-3.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 393.0 KiB
 lua-srpm-macros                  noarch  1-9.fc39                   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.3 KiB
 lz4-libs                         aarch64 1.9.4-4.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 261.4 KiB
 mpfr                             aarch64 4.2.1-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 818.7 KiB
 ncurses-base                     noarch  6.4-9.20240113.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 326.2 KiB
 ncurses-libs                     aarch64 6.4-9.20240113.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.2 MiB
 ocaml-srpm-macros                noarch  9-1.fc40                   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.9 KiB
 openblas-srpm-macros             noarch  2-14.fc39                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 104.0   B
 openldap                         aarch64 2.6.6-1.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.0 MiB
 openssl-libs                     aarch64 1:3.1.4-1.fc40             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   7.2 MiB
 p11-kit                          aarch64 0.25.3-1.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.8 MiB
 p11-kit-trust                    aarch64 0.25.3-1.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 655.6 KiB
 package-notes-srpm-macros        noarch  0.5-9.fc39                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.6 KiB
 pam                              aarch64 1.6.0-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  11.0 MiB
 pam-libs                         aarch64 1.6.0-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 607.0 KiB
 pcre2                            aarch64 10.42-2.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 841.5 KiB
 pcre2-syntax                     noarch  10.42-2.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 235.1 KiB
 perl-srpm-macros                 noarch  1-51.fc39                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 861.0   B
 pkgconf                          aarch64 1.9.5-2.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 235.7 KiB
 pkgconf-m4                       noarch  1.9.5-2.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  13.9 KiB
 pkgconf-pkg-config               aarch64 1.9.5-2.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 990.0   B
 popt                             aarch64 1.19-3.fc39                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 272.8 KiB
 publicsuffix-list-dafsa          noarch  20240107-1.fc40            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  67.5 KiB
 pyproject-srpm-macros            noarch  1.11.0-1.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.5 KiB
 python-srpm-macros               noarch  3.12-5.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  50.1 KiB
 qt5-srpm-macros                  noarch  5.15.12-1.fc40             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 492.0   B
 qt6-srpm-macros                  noarch  6.6.1-3.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 456.0   B
 readline                         aarch64 8.2-7.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 753.1 KiB
 rpm                              aarch64 4.19.1-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   4.0 MiB
 rpm-build-libs                   aarch64 4.19.1-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 262.4 KiB
 rpm-libs                         aarch64 4.19.1-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 861.7 KiB
 rpm-sequoia                      aarch64 1.5.0-2.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.2 MiB
 rust-srpm-macros                 noarch  25.2-2.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   5.1 KiB
 setup                            noarch  2.14.5-1.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 720.4 KiB
 sqlite-libs                      aarch64 3.45.0-1.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.5 MiB
 systemd-libs                     aarch64 255.2-2.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.5 MiB
 util-linux-core                  aarch64 2.39.3-2.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   6.1 MiB
 xxhash-libs                      aarch64 0.8.2-1.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 212.2 KiB
 xz-libs                          aarch64 5.4.5-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 265.6 KiB
 zig-srpm-macros                  noarch  1-1.fc40                   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 KiB
 zip                              aarch64 3.0-39.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 zlib-ng-compat                   aarch64 2.1.6-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 261.7 KiB
 zstd                             aarch64 1.5.5-4.fc39               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.6 MiB
Installing groups:                                                                                                                          
 Buildsystem building group                                                                                                                 

Transaction Summary:
 Installing:      152 packages

Total size of inbound packages is 52 MiB. Need to download 52 MiB.
After this operation 304 MiB will be used (install 304 MiB, remove 0 B).
[  1/152] bzip2-0:1.0.8-16.fc39.aarch64 100% |   1.8 MiB/s |  52.3 KiB |  00m00s
[  2/152] cpio-0:2.15-1.fc40.aarch64    100% |  15.5 MiB/s | 284.8 KiB |  00m00s
[  3/152] diffutils-0:3.10-3.fc39.aarch 100% |  23.6 MiB/s | 387.3 KiB |  00m00s
[  4/152] coreutils-0:9.4-3.fc40.aarch6 100% |  17.0 MiB/s |   1.2 MiB |  00m00s
[  5/152] fedora-release-common-0:40-0. 100% |   5.0 MiB/s |  20.5 KiB |  00m00s
[  6/152] bash-0:5.2.26-1.fc40.aarch64  100% |  24.4 MiB/s |   1.8 MiB |  00m00s
[  7/152] glibc-minimal-langpack-0:2.38 100% |  13.3 MiB/s |  95.4 KiB |  00m00s
[  8/152] findutils-1:4.9.0-6.fc40.aarc 100% |  36.5 MiB/s | 485.3 KiB |  00m00s
[  9/152] gzip-0:1.12-6.fc39.aarch64    100% |  30.8 MiB/s | 157.8 KiB |  00m00s
[ 10/152] grep-0:3.11-5.fc40.aarch64    100% |  27.8 MiB/s | 285.0 KiB |  00m00s
[ 11/152] info-0:7.1-1.fc40.aarch64     100% |  25.5 MiB/s | 182.9 KiB |  00m00s
[ 12/152] patch-0:2.7.6-22.fc39.aarch64 100% |  20.1 MiB/s | 123.3 KiB |  00m00s
[ 13/152] gawk-0:5.3.0-1.fc40.aarch64   100% |  36.1 MiB/s |   1.0 MiB |  00m00s
[ 14/152] redhat-rpm-config-0:280-1.fc4 100% |  14.7 MiB/s |  75.2 KiB |  00m00s
[ 15/152] rpm-build-0:4.19.1-2.fc40.aar 100% |  11.8 MiB/s |  72.4 KiB |  00m00s
[ 16/152] sed-0:4.8-14.fc39.aarch64     100% |  41.1 MiB/s | 294.8 KiB |  00m00s
[ 17/152] unzip-0:6.0-62.fc39.aarch64   100% |  25.5 MiB/s | 182.9 KiB |  00m00s
[ 18/152] tar-2:1.35-2.fc40.aarch64     100% |  51.6 MiB/s | 845.1 KiB |  00m00s
[ 19/152] shadow-utils-2:4.14.0-2.fc40. 100% |  57.1 MiB/s |   1.2 MiB |  00m00s
[ 20/152] which-0:2.21-40.fc39.aarch64  100% |   6.8 MiB/s |  41.8 KiB |  00m00s
[ 21/152] xz-0:5.4.5-1.fc40.aarch64     100% |  51.9 MiB/s | 531.3 KiB |  00m00s
[ 22/152] util-linux-0:2.39.3-2.fc40.aa 100% |  46.7 MiB/s |   1.1 MiB |  00m00s
[ 23/152] xz-libs-0:5.4.5-1.fc40.aarch6 100% |  13.0 MiB/s | 106.6 KiB |  00m00s
[ 24/152] audit-libs-0:4.0-5.fc40.aarch 100% |  19.7 MiB/s | 120.8 KiB |  00m00s
[ 25/152] glibc-0:2.38.9000-33.fc40.aar 100% |  74.4 MiB/s |   1.8 MiB |  00m00s
[ 26/152] authselect-libs-0:1.5.0-1.fc4 100% |  28.6 MiB/s | 234.3 KiB |  00m00s
[ 27/152] libblkid-0:2.39.3-2.fc40.aarc 100% |  18.9 MiB/s | 116.0 KiB |  00m00s
[ 28/152] libcap-ng-0:0.8.4-2.fc40.aarc 100% |   5.3 MiB/s |  32.5 KiB |  00m00s
[ 29/152] libmount-0:2.39.3-2.fc40.aarc 100% |  25.0 MiB/s | 153.6 KiB |  00m00s
[ 30/152] libfdisk-0:2.39.3-2.fc40.aarc 100% |  22.0 MiB/s | 157.9 KiB |  00m00s
[ 31/152] libsmartcols-0:2.39.3-2.fc40. 100% |  12.8 MiB/s |  65.7 KiB |  00m00s
[ 32/152] libselinux-0:3.6-2.fc40.aarch 100% |  14.2 MiB/s |  87.5 KiB |  00m00s
[ 33/152] libutempter-0:1.2.1-10.fc39.a 100% |   4.4 MiB/s |  26.8 KiB |  00m00s
[ 34/152] libuuid-0:2.39.3-2.fc40.aarch 100% |   4.6 MiB/s |  28.4 KiB |  00m00s
[ 35/152] pam-libs-0:1.6.0-1.fc40.aarch 100% |  11.1 MiB/s |  57.0 KiB |  00m00s
[ 36/152] ncurses-libs-0:6.4-9.20240113 100% |  26.8 MiB/s | 329.0 KiB |  00m00s
[ 37/152] pam-0:1.6.0-1.fc40.aarch64    100% |  39.5 MiB/s | 525.4 KiB |  00m00s
[ 38/152] readline-0:8.2-7.fc40.aarch64 100% |  23.2 MiB/s | 213.4 KiB |  00m00s
[ 39/152] systemd-libs-0:255.2-2.fc40.a 100% |  60.4 MiB/s | 680.0 KiB |  00m00s
[ 40/152] util-linux-core-0:2.39.3-2.fc 100% |  43.6 MiB/s | 491.3 KiB |  00m00s
[ 41/152] zlib-ng-compat-0:2.1.6-1.fc40 100% |  10.8 MiB/s |  66.2 KiB |  00m00s
[ 42/152] bzip2-libs-0:1.0.8-16.fc39.aa 100% |  10.4 MiB/s |  42.8 KiB |  00m00s
[ 43/152] libacl-0:2.3.2-1.fc40.aarch64 100% |   6.0 MiB/s |  24.7 KiB |  00m00s
[ 44/152] libcap-0:2.69-1.fc40.aarch64  100% |  13.6 MiB/s |  83.7 KiB |  00m00s
[ 45/152] libgcc-0:14.0.1-0.2.fc40.aarc 100% |  13.5 MiB/s |  82.8 KiB |  00m00s
[ 46/152] libzstd-0:1.5.5-4.fc39.aarch6 100% |  54.7 MiB/s | 280.3 KiB |  00m00s
[ 47/152] lz4-libs-0:1.9.4-4.fc39.aarch 100% |  16.6 MiB/s |  67.8 KiB |  00m00s
[ 48/152] libattr-0:2.5.2-1.fc40.aarch6 100% |   3.5 MiB/s |  17.8 KiB |  00m00s
[ 49/152] libeconf-0:0.5.2-1.fc40.aarch 100% |   5.9 MiB/s |  30.1 KiB |  00m00s
[ 50/152] libsemanage-0:3.6-1.fc40.aarc 100% |  18.5 MiB/s | 113.7 KiB |  00m00s
[ 51/152] setup-0:2.14.5-1.fc40.noarch  100% |  28.9 MiB/s | 148.1 KiB |  00m00s
[ 52/152] libxcrypt-0:4.4.36-4.fc40.aar 100% |  13.3 MiB/s | 122.6 KiB |  00m00s
[ 53/152] debugedit-0:5.0-12.fc40.aarch 100% |  12.7 MiB/s |  78.1 KiB |  00m00s
[ 54/152] elfutils-libelf-0:0.190-4.fc4 100% |  21.0 MiB/s | 193.9 KiB |  00m00s
[ 55/152] elfutils-0:0.190-4.fc40.aarch 100% |  35.6 MiB/s | 546.2 KiB |  00m00s
[ 56/152] pkgconf-pkg-config-0:1.9.5-2. 100% |   2.4 MiB/s |   9.6 KiB |  00m00s
[ 57/152] file-0:5.45-1.fc40.aarch64    100% |   6.0 MiB/s |  49.4 KiB |  00m00s
[ 58/152] popt-0:1.19-3.fc39.aarch64    100% |  11.5 MiB/s |  59.1 KiB |  00m00s
[ 59/152] rpm-0:4.19.1-2.fc40.aarch64   100% |  49.8 MiB/s | 509.6 KiB |  00m00s
[ 60/152] rpm-build-libs-0:4.19.1-2.fc4 100% |  12.8 MiB/s |  92.0 KiB |  00m00s
[ 61/152] rpm-libs-0:4.19.1-2.fc40.aarc 100% |  37.3 MiB/s | 305.7 KiB |  00m00s
[ 62/152] zstd-0:1.5.5-4.fc39.aarch64   100% |  54.4 MiB/s | 445.7 KiB |  00m00s
[ 63/152] libarchive-0:3.7.2-1.fc40.aar 100% |  43.6 MiB/s | 402.3 KiB |  00m00s
[ 64/152] ansible-srpm-macros-0:1-12.fc 100% |   4.1 MiB/s |  20.9 KiB |  00m00s
[ 65/152] glibc-gconv-extra-0:2.38.9000 100% | 110.4 MiB/s |   2.0 MiB |  00m00s
[ 66/152] binutils-0:2.41-30.fc40.aarch 100% |  95.2 MiB/s |   6.8 MiB |  00m00s
[ 67/152] dwz-0:0.15-3.fc39.aarch64     100% |  13.3 MiB/s | 135.7 KiB |  00m00s
[ 68/152] efi-srpm-macros-0:5-9.fc39.no 100% |   2.0 MiB/s |  22.2 KiB |  00m00s
[ 69/152] fonts-srpm-macros-1:2.0.5-12. 100% |   6.5 MiB/s |  26.5 KiB |  00m00s
[ 70/152] forge-srpm-macros-0:0.2.0-1.f 100% |   3.6 MiB/s |  18.5 KiB |  00m00s
[ 71/152] fpc-srpm-macros-0:1.3-8.fc39. 100% |   1.8 MiB/s |   7.4 KiB |  00m00s
[ 72/152] ghc-srpm-macros-0:1.6.1-3.fc4 100% |   2.0 MiB/s |   8.1 KiB |  00m00s
[ 73/152] gnat-srpm-macros-0:6-3.fc39.n 100% |   2.9 MiB/s |   8.8 KiB |  00m00s
[ 74/152] kernel-srpm-macros-0:1.0-20.f 100% |   2.6 MiB/s |  10.5 KiB |  00m00s
[ 75/152] lua-srpm-macros-0:1-9.fc39.no 100% |   2.1 MiB/s |   8.6 KiB |  00m00s
[ 76/152] go-srpm-macros-0:3.3.1-1.fc40 100% |   4.5 MiB/s |  27.7 KiB |  00m00s
[ 77/152] ocaml-srpm-macros-0:9-1.fc40. 100% |   2.2 MiB/s |   9.0 KiB |  00m00s
[ 78/152] openblas-srpm-macros-0:2-14.f 100% |   1.8 MiB/s |   7.5 KiB |  00m00s
[ 79/152] package-notes-srpm-macros-0:0 100% |   3.6 MiB/s |  11.2 KiB |  00m00s
[ 80/152] pyproject-srpm-macros-0:1.11. 100% |   3.6 MiB/s |  14.8 KiB |  00m00s
[ 81/152] perl-srpm-macros-0:1-51.fc39. 100% |   2.0 MiB/s |   8.0 KiB |  00m00s
[ 82/152] python-srpm-macros-0:3.12-5.f 100% |   6.1 MiB/s |  24.9 KiB |  00m00s
[ 83/152] qt6-srpm-macros-0:6.6.1-3.fc4 100% |   2.1 MiB/s |   8.8 KiB |  00m00s
[ 84/152] rust-srpm-macros-0:25.2-2.fc4 100% |   2.5 MiB/s |  13.0 KiB |  00m00s
[ 85/152] qt5-srpm-macros-0:5.15.12-1.f 100% |   1.4 MiB/s |   8.4 KiB |  00m00s
[ 86/152] zig-srpm-macros-0:1-1.fc40.no 100% |   1.9 MiB/s |   8.0 KiB |  00m00s
[ 87/152] pkgconf-0:1.9.5-2.fc39.aarch6 100% |  10.3 MiB/s |  42.3 KiB |  00m00s
[ 88/152] pkgconf-m4-0:1.9.5-2.fc39.noa 100% |   3.4 MiB/s |  13.9 KiB |  00m00s
[ 89/152] zip-0:3.0-39.fc40.aarch64     100% |  32.0 MiB/s | 262.1 KiB |  00m00s
[ 90/152] libpkgconf-0:1.9.5-2.fc39.aar 100% |   9.3 MiB/s |  38.1 KiB |  00m00s
[ 91/152] authselect-0:1.5.0-1.fc40.aar 100% |  12.8 MiB/s | 143.8 KiB |  00m00s
[ 92/152] ed-0:1.20-1.fc40.aarch64      100% |   6.6 MiB/s |  81.2 KiB |  00m00s
[ 93/152] gdbm-1:1.23-4.fc39.aarch64    100% |  13.2 MiB/s | 148.4 KiB |  00m00s
[ 94/152] gdbm-libs-1:1.23-4.fc39.aarch 100% |  11.0 MiB/s |  56.2 KiB |  00m00s
[ 95/152] libnsl2-0:2.0.0-6.fc39.aarch6 100% |   4.9 MiB/s |  30.0 KiB |  00m00s
[ 96/152] libpwquality-0:1.4.5-6.fc39.a 100% |  15.2 MiB/s | 108.9 KiB |  00m00s
[ 97/152] libtirpc-0:1.3.4-1.rc1.fc40.a 100% |  15.5 MiB/s |  95.4 KiB |  00m00s
[ 98/152] ca-certificates-0:2023.2.62_v 100% | 105.3 MiB/s | 862.6 KiB |  00m00s
[ 99/152] crypto-policies-0:20231204-1. 100% |  11.2 MiB/s |  68.7 KiB |  00m00s
[100/152] ncurses-base-0:6.4-9.20240113 100% |  12.4 MiB/s |  63.5 KiB |  00m00s
[101/152] openssl-libs-1:3.1.4-1.fc40.a 100% | 107.5 MiB/s |   2.0 MiB |  00m00s
[102/152] krb5-libs-0:1.21.2-3.fc40.aar 100% |  83.3 MiB/s | 767.8 KiB |  00m00s
[103/152] libcom_err-0:1.47.0-2.fc39.aa 100% |   3.6 MiB/s |  26.1 KiB |  00m00s
[104/152] libsepol-0:3.6-1.fc40.aarch64 100% |  39.5 MiB/s | 323.5 KiB |  00m00s
[105/152] cracklib-0:2.9.11-2.fc39.aarc 100% |  13.5 MiB/s |  83.2 KiB |  00m00s
[106/152] pcre2-0:10.42-2.fc40.aarch64  100% |  21.4 MiB/s | 219.1 KiB |  00m00s
[107/152] keyutils-libs-0:1.6.3-1.fc40. 100% |   5.1 MiB/s |  31.5 KiB |  00m00s
[108/152] libverto-0:0.3.2-6.fc39.aarch 100% |   5.0 MiB/s |  20.5 KiB |  00m00s
[109/152] libxml2-0:2.12.4-1.fc40.aarch 100% |  74.0 MiB/s | 682.2 KiB |  00m00s
[110/152] basesystem-0:11-18.fc39.noarc 100% |   1.8 MiB/s |   7.2 KiB |  00m00s
[111/152] glibc-common-0:2.38.9000-33.f 100% |  33.0 MiB/s | 371.6 KiB |  00m00s
[112/152] filesystem-0:3.18-6.fc39.aarc 100% | 106.9 MiB/s |   1.1 MiB |  00m00s
[113/152] gmp-1:6.2.1-5.fc39.aarch64    100% |  37.2 MiB/s | 266.4 KiB |  00m00s
[114/152] fedora-repos-0:40-0.2.noarch  100% |   3.0 MiB/s |   9.3 KiB |  00m00s
[115/152] mpfr-0:4.2.1-1.fc40.aarch64   100% |  39.1 MiB/s | 320.2 KiB |  00m00s
[116/152] elfutils-libs-0:0.190-4.fc40. 100% |  42.1 MiB/s | 258.7 KiB |  00m00s
[117/152] file-libs-0:5.45-1.fc40.aarch 100% |  53.1 MiB/s | 761.4 KiB |  00m00s
[118/152] libstdc++-0:14.0.1-0.2.fc40.a 100% |  72.1 MiB/s | 812.4 KiB |  00m00s
[119/152] coreutils-common-0:9.4-3.fc40 100% | 125.0 MiB/s |   2.1 MiB |  00m00s
[120/152] p11-kit-trust-0:0.25.3-1.fc40 100% |  17.2 MiB/s | 140.6 KiB |  00m00s
[121/152] p11-kit-0:0.25.3-1.fc40.aarch 100% |  31.3 MiB/s | 481.0 KiB |  00m00s
[122/152] elfutils-debuginfod-client-0: 100% |   9.1 MiB/s |  37.3 KiB |  00m00s
[123/152] alternatives-0:1.26-1.fc40.aa 100% |   7.5 MiB/s |  38.5 KiB |  00m00s
[124/152] jansson-0:2.13.1-7.fc39.aarch 100% |  11.1 MiB/s |  45.5 KiB |  00m00s
[125/152] lua-libs-0:5.4.6-3.fc39.aarch 100% |  25.6 MiB/s | 130.9 KiB |  00m00s
[126/152] binutils-gold-0:2.41-30.fc40. 100% |  62.7 MiB/s | 963.0 KiB |  00m00s
[127/152] sqlite-libs-0:3.45.0-1.fc40.a 100% |  86.0 MiB/s | 704.6 KiB |  00m00s
[128/152] rpm-sequoia-0:1.5.0-2.fc40.aa 100% |  81.9 MiB/s | 838.8 KiB |  00m00s
[129/152] libgomp-0:14.0.1-0.2.fc40.aar 100% |  38.9 MiB/s | 318.5 KiB |  00m00s
[130/152] pcre2-syntax-0:10.42-2.fc40.n 100% |  28.0 MiB/s | 143.1 KiB |  00m00s
[131/152] libtasn1-0:4.19.0-3.fc39.aarc 100% |  17.9 MiB/s |  73.1 KiB |  00m00s
[132/152] fedora-repos-rawhide-0:40-0.2 100% |   2.9 MiB/s |   8.9 KiB |  00m00s
[133/152] libffi-0:3.4.4-5.fc40.aarch64 100% |   6.1 MiB/s |  37.4 KiB |  00m00s
[134/152] fedora-gpg-keys-0:40-0.2.noar 100% |  23.3 MiB/s | 119.4 KiB |  00m00s
[135/152] elfutils-default-yama-scope-0 100% |   3.1 MiB/s |  12.8 KiB |  00m00s
[136/152] fedora-release-0:40-0.29.noar 100% |   3.3 MiB/s |  10.0 KiB |  00m00s
[137/152] fedora-release-identity-basic 100% |   3.5 MiB/s |  10.8 KiB |  00m00s
[138/152] curl-0:8.5.0-2.fc40.aarch64   100% |  40.0 MiB/s | 369.1 KiB |  00m00s
[139/152] libcurl-0:8.5.0-2.fc40.aarch6 100% |  55.3 MiB/s | 339.8 KiB |  00m00s
[140/152] libnghttp2-0:1.59.0-1.fc40.aa 100% |  12.3 MiB/s |  75.8 KiB |  00m00s
[141/152] xxhash-libs-0:0.8.2-1.fc39.aa 100% |   8.5 MiB/s |  34.8 KiB |  00m00s
[142/152] libidn2-0:2.3.4-3.fc39.aarch6 100% |  27.2 MiB/s | 111.4 KiB |  00m00s
[143/152] libbrotli-0:1.1.0-1.fc40.aarc 100% |  42.0 MiB/s | 344.4 KiB |  00m00s
[144/152] libpsl-0:0.21.5-1.fc40.aarch6 100% |  10.4 MiB/s |  63.7 KiB |  00m00s
[145/152] libssh-0:0.10.6-2.fc40.aarch6 100% |  29.7 MiB/s | 213.2 KiB |  00m00s
[146/152] openldap-0:2.6.6-1.fc39.aarch 100% |  49.0 MiB/s | 251.1 KiB |  00m00s
[147/152] libevent-0:2.1.12-9.fc39.aarc 100% |  49.5 MiB/s | 253.5 KiB |  00m00s
[148/152] libssh-config-0:0.10.6-2.fc40 100% |   2.2 MiB/s |   9.1 KiB |  00m00s
[149/152] cyrus-sasl-lib-0:2.1.28-17.fc 100% |  58.5 MiB/s | 778.4 KiB |  00m00s
[150/152] publicsuffix-list-dafsa-0:202 100% |  14.2 MiB/s |  58.0 KiB |  00m00s
[151/152] gdb-minimal-0:14.1-6.fc40.aar 100% |  65.5 MiB/s |   3.9 MiB |  00m00s
[152/152] libunistring-0:1.1-5.fc40.aar 100% |  40.5 MiB/s | 539.8 KiB |  00m00s
--------------------------------------------------------------------------------
[152/152] Total                         100% |  99.5 MiB/s |  51.7 MiB |  00m01s
Running transaction
[  1/154] Verify package files          100% | 752.0   B/s | 152.0   B |  00m00s
>>> Running pre-transaction scriptlet: filesystem-0:3.18-6.fc39.aarch64
>>> Stop pre-transaction scriptlet: filesystem-0:3.18-6.fc39.aarch64
[  2/154] Prepare transaction           100% |   2.5 KiB/s | 152.0   B |  00m00s
[  3/154] Installing libgcc-0:14.0.1-0. 100% | 171.8 MiB/s | 351.8 KiB |  00m00s
>>> Running post-install scriptlet: libgcc-0:14.0.1-0.2.fc40.aarch64
>>> Stop post-install scriptlet: libgcc-0:14.0.1-0.2.fc40.aarch64
[  4/154] Installing crypto-policies-0: 100% |  22.2 MiB/s | 181.7 KiB |  00m00s
>>> Running post-install scriptlet: crypto-policies-0:20231204-1.git1e3a2e4.fc40
>>> Stop post-install scriptlet: crypto-policies-0:20231204-1.git1e3a2e4.fc40.no
[  5/154] Installing fedora-release-ide 100% |   0.0   B/s | 952.0   B |  00m00s
[  6/154] Installing fedora-gpg-keys-0: 100% |  32.7 MiB/s | 167.6 KiB |  00m00s
[  7/154] Installing fedora-repos-rawhi 100% |   0.0   B/s |   2.4 KiB |  00m00s
[  8/154] Installing fedora-repos-0:40- 100% |   0.0   B/s |   5.7 KiB |  00m00s
[  9/154] Installing fedora-release-com 100% |  22.6 MiB/s |  23.2 KiB |  00m00s
[ 10/154] Installing fedora-release-0:4 100% |   0.0   B/s | 124.0   B |  00m00s
[ 11/154] Installing setup-0:2.14.5-1.f 100% |  44.3 MiB/s | 725.8 KiB |  00m00s
>>> Running post-install scriptlet: setup-0:2.14.5-1.fc40.noarch
>>> Stop post-install scriptlet: setup-0:2.14.5-1.fc40.noarch
[ 12/154] Installing filesystem-0:3.18- 100% |   2.1 MiB/s | 212.4 KiB |  00m00s
[ 13/154] Installing basesystem-0:11-18 100% |   0.0   B/s | 124.0   B |  00m00s
[ 14/154] Installing publicsuffix-list- 100% |  66.7 MiB/s |  68.3 KiB |  00m00s
[ 15/154] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
[ 16/154] Installing pcre2-syntax-0:10. 100% | 232.0 MiB/s | 237.6 KiB |  00m00s
[ 17/154] Installing coreutils-common-0 100% | 293.9 MiB/s |  11.5 MiB |  00m00s
[ 18/154] Installing ncurses-base-0:6.4 100% |  57.2 MiB/s | 351.6 KiB |  00m00s
[ 19/154] Installing glibc-minimal-lang 100% |   0.0   B/s | 124.0   B |  00m00s
[ 20/154] Installing ncurses-libs-0:6.4 100% | 374.6 MiB/s |   2.2 MiB |  00m00s
>>> Running pre-install scriptlet: glibc-0:2.38.9000-33.fc40.aarch64
>>> Stop pre-install scriptlet: glibc-0:2.38.9000-33.fc40.aarch64
[ 21/154] Installing glibc-0:2.38.9000- 100% | 256.5 MiB/s |   9.7 MiB |  00m00s
>>> Running post-install scriptlet: glibc-0:2.38.9000-33.fc40.aarch64
>>> Stop post-install scriptlet: glibc-0:2.38.9000-33.fc40.aarch64
[ 22/154] Installing bash-0:5.2.26-1.fc 100% | 319.7 MiB/s |   8.3 MiB |  00m00s
>>> Running post-install scriptlet: bash-0:5.2.26-1.fc40.aarch64
>>> Stop post-install scriptlet: bash-0:5.2.26-1.fc40.aarch64
[ 23/154] Installing glibc-common-0:2.3 100% | 320.3 MiB/s |   2.6 MiB |  00m00s
[ 24/154] Installing glibc-gconv-extra- 100% | 527.4 MiB/s |  49.0 MiB |  00m00s
>>> Running post-install scriptlet: glibc-gconv-extra-0:2.38.9000-33.fc40.aarch6
>>> Stop post-install scriptlet: glibc-gconv-extra-0:2.38.9000-33.fc40.aarch64
[ 25/154] Installing zlib-ng-compat-0:2 100% | 256.3 MiB/s | 262.5 KiB |  00m00s
[ 26/154] Installing xz-libs-0:5.4.5-1. 100% | 260.5 MiB/s | 266.7 KiB |  00m00s
[ 27/154] Installing bzip2-libs-0:1.0.8 100% | 197.1 MiB/s | 201.8 KiB |  00m00s
[ 28/154] Installing libuuid-0:2.39.3-2 100% | 194.1 MiB/s | 198.8 KiB |  00m00s
[ 29/154] Installing readline-0:8.2-7.f 100% | 368.8 MiB/s | 755.2 KiB |  00m00s
[ 30/154] Installing libzstd-0:1.5.5-4. 100% | 259.5 MiB/s | 797.2 KiB |  00m00s
[ 31/154] Installing elfutils-libelf-0: 100% | 376.8 MiB/s |   1.1 MiB |  00m00s
[ 32/154] Installing popt-0:1.19-3.fc39 100% |  91.0 MiB/s | 279.5 KiB |  00m00s
[ 33/154] Installing libstdc++-0:14.0.1 100% | 307.8 MiB/s |   2.8 MiB |  00m00s
[ 34/154] Installing libblkid-0:2.39.3- 100% | 384.6 MiB/s | 393.9 KiB |  00m00s
[ 35/154] Installing libattr-0:2.5.2-1. 100% | 192.8 MiB/s | 197.5 KiB |  00m00s
[ 36/154] Installing libacl-0:2.3.2-1.f 100% | 192.2 MiB/s | 196.8 KiB |  00m00s
[ 37/154] Installing libxcrypt-0:4.4.36 100% | 196.1 MiB/s | 401.6 KiB |  00m00s
[ 38/154] Installing gmp-1:6.2.1-5.fc39 100% | 353.3 MiB/s | 723.5 KiB |  00m00s
[ 39/154] Installing lz4-libs-0:1.9.4-4 100% | 256.3 MiB/s | 262.5 KiB |  00m00s
[ 40/154] Installing libeconf-0:0.5.2-1 100% | 200.8 MiB/s | 205.7 KiB |  00m00s
[ 41/154] Installing gdbm-libs-1:1.23-4 100% | 208.7 MiB/s | 427.5 KiB |  00m00s
[ 42/154] Installing mpfr-0:4.2.1-1.fc4 100% | 267.0 MiB/s | 820.2 KiB |  00m00s
[ 43/154] Installing gawk-0:5.3.0-1.fc4 100% | 387.5 MiB/s |   4.3 MiB |  00m00s
[ 44/154] Installing dwz-0:0.15-3.fc39. 100% | 379.0 MiB/s | 388.1 KiB |  00m00s
[ 45/154] Installing unzip-0:6.0-62.fc3 100% | 237.7 MiB/s | 730.2 KiB |  00m00s
[ 46/154] Installing file-libs-0:5.45-1 100% | 589.6 MiB/s |  10.0 MiB |  00m00s
[ 47/154] Installing file-0:5.45-1.fc40 100% | 131.3 MiB/s | 268.9 KiB |  00m00s
[ 48/154] Installing libcap-ng-0:0.8.4- 100% | 409.0 MiB/s | 418.9 KiB |  00m00s
[ 49/154] Installing audit-libs-0:4.0-5 100% | 268.2 MiB/s | 549.3 KiB |  00m00s
[ 50/154] Installing pam-libs-0:1.6.0-1 100% | 297.5 MiB/s | 609.2 KiB |  00m00s
[ 51/154] Installing libcap-0:2.69-1.fc 100% | 343.1 MiB/s |   1.4 MiB |  00m00s
[ 52/154] Installing systemd-libs-0:255 100% | 351.1 MiB/s |   2.5 MiB |  00m00s
[ 53/154] Installing libsmartcols-0:2.3 100% | 282.6 MiB/s | 289.4 KiB |  00m00s
[ 54/154] Installing libcom_err-0:1.47. 100% | 234.7 MiB/s | 240.3 KiB |  00m00s
[ 55/154] Installing libsepol-0:3.6-1.f 100% | 284.8 MiB/s | 875.1 KiB |  00m00s
[ 56/154] Installing pcre2-0:10.42-2.fc 100% | 411.6 MiB/s | 842.9 KiB |  00m00s
[ 57/154] Installing libselinux-0:3.6-2 100% | 260.0 MiB/s | 266.2 KiB |  00m00s
[ 58/154] Installing sed-0:4.8-14.fc39. 100% | 185.5 MiB/s | 949.8 KiB |  00m00s
[ 59/154] Installing grep-0:3.11-5.fc40 100% | 156.7 MiB/s |   1.1 MiB |  00m00s
[ 60/154] Installing findutils-1:4.9.0- 100% | 237.3 MiB/s |   1.7 MiB |  00m00s
[ 61/154] Installing xz-0:5.4.5-1.fc40. 100% | 228.3 MiB/s |   2.3 MiB |  00m00s
[ 62/154] Installing libmount-0:2.39.3- 100% | 237.0 MiB/s | 485.5 KiB |  00m00s
[ 63/154] Installing alternatives-0:1.2 100% | 214.7 MiB/s | 219.9 KiB |  00m00s
[ 64/154] Installing jansson-0:2.13.1-7 100% | 216.6 MiB/s | 221.8 KiB |  00m00s
[ 65/154] Installing lua-libs-0:5.4.6-3 100% | 384.9 MiB/s | 394.2 KiB |  00m00s
[ 66/154] Installing libtasn1-0:4.19.0- 100% | 278.8 MiB/s | 285.5 KiB |  00m00s
[ 67/154] Installing libunistring-0:1.1 100% | 374.2 MiB/s |   1.9 MiB |  00m00s
[ 68/154] Installing libidn2-0:2.3.4-3. 100% | 148.8 MiB/s | 457.0 KiB |  00m00s
[ 69/154] Installing libpsl-0:0.21.5-1. 100% | 193.0 MiB/s | 197.6 KiB |  00m00s
[ 70/154] Installing util-linux-core-0: 100% | 469.0 MiB/s |   6.1 MiB |  00m00s
[ 71/154] Installing tar-2:1.35-2.fc40. 100% | 278.9 MiB/s |   3.1 MiB |  00m00s
[ 72/154] Installing libsemanage-0:3.6- 100% | 177.3 MiB/s | 363.2 KiB |  00m00s
[ 73/154] Installing shadow-utils-2:4.1 100% | 163.4 MiB/s |   7.2 MiB |  00m00s
>>> Running pre-install scriptlet: libutempter-0:1.2.1-10.fc39.aarch64
>>> Stop pre-install scriptlet: libutempter-0:1.2.1-10.fc39.aarch64
[ 74/154] Installing libutempter-0:1.2. 100% | 204.9 MiB/s | 419.6 KiB |  00m00s
[ 75/154] Installing zip-0:3.0-39.fc40. 100% | 281.0 MiB/s |   1.1 MiB |  00m00s
[ 76/154] Installing gdbm-1:1.23-4.fc39 100% | 227.8 MiB/s | 933.2 KiB |  00m00s
[ 77/154] Installing cyrus-sasl-lib-0:2 100% | 345.2 MiB/s |   3.1 MiB |  00m00s
[ 78/154] Installing zstd-0:1.5.5-4.fc3 100% | 260.0 MiB/s |   1.6 MiB |  00m00s
[ 79/154] Installing libfdisk-0:2.39.3- 100% | 242.3 MiB/s | 496.2 KiB |  00m00s
[ 80/154] Installing bzip2-0:1.0.8-16.f 100% | 211.0 MiB/s | 432.0 KiB |  00m00s
[ 81/154] Installing libxml2-0:2.12.4-1 100% | 367.2 MiB/s |   2.2 MiB |  00m00s
[ 82/154] Installing sqlite-libs-0:3.45 100% | 299.1 MiB/s |   1.5 MiB |  00m00s
[ 83/154] Installing ed-0:1.20-1.fc40.a 100% | 277.9 MiB/s | 284.6 KiB |  00m00s
[ 84/154] Installing patch-0:2.7.6-22.f 100% | 320.3 MiB/s | 328.0 KiB |  00m00s
[ 85/154] Installing elfutils-default-y 100% | 255.4 KiB/s |   2.0 KiB |  00m00s
>>> Running post-install scriptlet: elfutils-default-yama-scope-0:0.190-4.fc40.n
>>> Stop post-install scriptlet: elfutils-default-yama-scope-0:0.190-4.fc40.noar
[ 86/154] Installing cpio-0:2.15-1.fc40 100% | 203.4 MiB/s |   1.2 MiB |  00m00s
[ 87/154] Installing diffutils-0:3.10-3 100% | 263.6 MiB/s |   2.1 MiB |  00m00s
[ 88/154] Installing libpkgconf-0:1.9.5 100% | 194.4 MiB/s | 199.1 KiB |  00m00s
[ 89/154] Installing pkgconf-0:1.9.5-2. 100% | 116.3 MiB/s | 238.3 KiB |  00m00s
[ 90/154] Installing keyutils-libs-0:1. 100% | 222.4 MiB/s | 227.8 KiB |  00m00s
[ 91/154] Installing libverto-0:0.3.2-6 100% | 194.6 MiB/s | 199.2 KiB |  00m00s
[ 92/154] Installing libgomp-0:14.0.1-0 100% | 275.9 MiB/s | 564.9 KiB |  00m00s
[ 93/154] Installing libffi-0:3.4.4-5.f 100% | 276.2 MiB/s | 282.8 KiB |  00m00s
[ 94/154] Installing p11-kit-0:0.25.3-1 100% | 217.8 MiB/s |   2.8 MiB |  00m00s
[ 95/154] Installing p11-kit-trust-0:0. 100% |  58.4 MiB/s | 657.3 KiB |  00m00s
>>> Running post-install scriptlet: p11-kit-trust-0:0.25.3-1.fc40.aarch64
>>> Stop post-install scriptlet: p11-kit-trust-0:0.25.3-1.fc40.aarch64
[ 96/154] Installing openssl-libs-1:3.1 100% | 327.1 MiB/s |   7.2 MiB |  00m00s
[ 97/154] Installing coreutils-0:9.4-3. 100% | 433.2 MiB/s |  20.8 MiB |  00m00s
>>> Running pre-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-4.fc40.n
>>> Stop pre-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-4.fc40.noar
[ 98/154] Installing ca-certificates-0: 100% |   2.4 MiB/s |   2.3 MiB |  00m01s
>>> Running post-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-4.fc40.
>>> Stop post-install scriptlet: ca-certificates-0:2023.2.62_v7.0.401-4.fc40.noa
[ 99/154] Installing krb5-libs-0:1.21.2 100% | 283.9 MiB/s |   3.4 MiB |  00m00s
[100/154] Installing libtirpc-0:1.3.4-1 100% | 270.0 MiB/s | 276.4 KiB |  00m00s
[101/154] Installing gzip-0:1.12-6.fc39 100% | 156.7 MiB/s | 481.4 KiB |  00m00s
>>> Running pre-install scriptlet: authselect-libs-0:1.5.0-1.fc40.aarch64
>>> Stop pre-install scriptlet: authselect-libs-0:1.5.0-1.fc40.aarch64
[102/154] Installing authselect-libs-0: 100% | 155.7 MiB/s |   1.1 MiB |  00m00s
[103/154] Installing authselect-0:1.5.0 100% | 103.1 MiB/s | 316.8 KiB |  00m00s
[104/154] Installing cracklib-0:2.9.11- 100% | 154.0 MiB/s | 946.1 KiB |  00m00s
[105/154] Installing libpwquality-0:1.4 100% | 158.2 MiB/s |   1.1 MiB |  00m00s
[106/154] Installing libnsl2-0:2.0.0-6. 100% | 217.8 MiB/s | 223.0 KiB |  00m00s
[107/154] Installing pam-0:1.6.0-1.fc40 100% | 355.7 MiB/s |  11.0 MiB |  00m00s
[108/154] Installing libssh-0:0.10.6-2. 100% | 284.8 MiB/s | 583.2 KiB |  00m00s
[109/154] Installing libarchive-0:3.7.2 100% | 338.7 MiB/s |   1.0 MiB |  00m00s
[110/154] Installing rpm-sequoia-0:1.5. 100% | 320.5 MiB/s |   2.2 MiB |  00m00s
[111/154] Installing rpm-libs-0:4.19.1- 100% | 281.0 MiB/s | 863.2 KiB |  00m00s
[112/154] Installing libevent-0:2.1.12- 100% | 380.7 MiB/s |   1.5 MiB |  00m00s
[113/154] Installing openldap-0:2.6.6-1 100% | 248.3 MiB/s |   1.0 MiB |  00m00s
[114/154] Installing libnghttp2-0:1.59. 100% | 257.0 MiB/s | 263.2 KiB |  00m00s
[115/154] Installing xxhash-libs-0:0.8. 100% | 208.6 MiB/s | 213.6 KiB |  00m00s
[116/154] Installing libbrotli-0:1.1.0- 100% | 285.1 MiB/s |   1.1 MiB |  00m00s
[117/154] Installing libcurl-0:8.5.0-2. 100% | 279.2 MiB/s | 857.6 KiB |  00m00s
[118/154] Installing elfutils-debuginfo 100% | 389.4 MiB/s | 398.8 KiB |  00m00s
[119/154] Installing elfutils-libs-0:0. 100% | 326.8 MiB/s |   1.0 MiB |  00m00s
[120/154] Installing binutils-gold-0:2. 100% | 170.7 MiB/s |   3.1 MiB |  00m00s
>>> Running post-install scriptlet: binutils-gold-0:2.41-30.fc40.aarch64
>>> Stop post-install scriptlet: binutils-gold-0:2.41-30.fc40.aarch64
[121/154] Installing binutils-0:2.41-30 100% | 349.0 MiB/s |  32.8 MiB |  00m00s
>>> Running post-install scriptlet: binutils-0:2.41-30.fc40.aarch64
>>> Stop post-install scriptlet: binutils-0:2.41-30.fc40.aarch64
[122/154] Installing elfutils-0:0.190-4 100% | 385.8 MiB/s |   5.0 MiB |  00m00s
[123/154] Installing gdb-minimal-0:14.1 100% | 357.3 MiB/s |  12.1 MiB |  00m00s
[124/154] Installing debugedit-0:5.0-12 100% | 244.9 MiB/s | 501.5 KiB |  00m00s
[125/154] Installing rpm-build-libs-0:4 100% | 257.0 MiB/s | 263.2 KiB |  00m00s
[126/154] Installing curl-0:8.5.0-2.fc4 100% |  56.4 MiB/s | 924.7 KiB |  00m00s
>>> Running pre-install scriptlet: rpm-0:4.19.1-2.fc40.aarch64
>>> Stop pre-install scriptlet: rpm-0:4.19.1-2.fc40.aarch64
[127/154] Installing rpm-0:4.19.1-2.fc4 100% | 156.1 MiB/s |   3.4 MiB |  00m00s
[128/154] Installing efi-srpm-macros-0: 100% |  40.2 MiB/s |  41.2 KiB |  00m00s
[129/154] Installing lua-srpm-macros-0: 100% |   0.0   B/s |   1.9 KiB |  00m00s
[130/154] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.7 KiB |  00m00s
[131/154] Installing pkgconf-m4-0:1.9.5 100% |   0.0   B/s |  14.3 KiB |  00m00s
[132/154] Installing pkgconf-pkg-config 100% |   0.0   B/s |   1.8 KiB |  00m00s
[133/154] Installing rust-srpm-macros-0 100% |   0.0   B/s |   5.8 KiB |  00m00s
[134/154] Installing qt6-srpm-macros-0: 100% |   0.0   B/s | 732.0   B |  00m00s
[135/154] Installing qt5-srpm-macros-0: 100% |   0.0   B/s | 768.0   B |  00m00s
[136/154] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[137/154] Installing package-notes-srpm 100% |   0.0   B/s |   2.0 KiB |  00m00s
[138/154] Installing openblas-srpm-macr 100% |   0.0   B/s | 384.0   B |  00m00s
[139/154] Installing ocaml-srpm-macros- 100% |   0.0   B/s |   2.2 KiB |  00m00s
[140/154] Installing kernel-srpm-macros 100% |   0.0   B/s |   2.3 KiB |  00m00s
[141/154] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[142/154] Installing ghc-srpm-macros-0: 100% |   0.0   B/s | 648.0   B |  00m00s
[143/154] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[144/154] Installing ansible-srpm-macro 100% |   0.0   B/s |  36.2 KiB |  00m00s
[145/154] Installing fonts-srpm-macros- 100% |  55.1 MiB/s |  56.5 KiB |  00m00s
[146/154] Installing forge-srpm-macros- 100% |  37.7 MiB/s |  38.6 KiB |  00m00s
[147/154] Installing go-srpm-macros-0:3 100% |  60.2 MiB/s |  61.6 KiB |  00m00s
[148/154] Installing python-srpm-macros 100% |  50.1 MiB/s |  51.3 KiB |  00m00s
[149/154] Installing redhat-rpm-config- 100% |  92.6 MiB/s | 189.6 KiB |  00m00s
[150/154] Installing rpm-build-0:4.19.1 100% | 301.1 MiB/s |   1.2 MiB |  00m00s
[151/154] Installing pyproject-srpm-mac 100% |   2.0 MiB/s |   2.1 KiB |  00m00s
[152/154] Installing util-linux-0:2.39. 100% | 425.8 MiB/s |  16.6 MiB |  00m00s
[153/154] Installing which-0:2.21-40.fc 100% | 244.4 MiB/s | 250.3 KiB |  00m00s
[154/154] Installing info-0:7.1-1.fc40. 100% | 468.7 KiB/s | 613.9 KiB |  00m01s
>>> Running post-transaction scriptlet: filesystem-0:3.18-6.fc39.aarch64
>>> Stop post-transaction scriptlet: filesystem-0:3.18-6.fc39.aarch64
>>> Running post-transaction scriptlet: ca-certificates-0:2023.2.62_v7.0.401-4.f
>>> Stop post-transaction scriptlet: ca-certificates-0:2023.2.62_v7.0.401-4.fc40
>>> Running post-transaction scriptlet: authselect-libs-0:1.5.0-1.fc40.aarch64
>>> Stop post-transaction scriptlet: authselect-libs-0:1.5.0-1.fc40.aarch64
>>> Running post-transaction scriptlet: rpm-0:4.19.1-2.fc40.aarch64
>>> Stop post-transaction scriptlet: rpm-0:4.19.1-2.fc40.aarch64
>>> Running trigger-install scriptlet: glibc-common-0:2.38.9000-33.fc40.aarch64
>>> Stop trigger-install scriptlet: glibc-common-0:2.38.9000-33.fc40.aarch64
>>> Running trigger-install scriptlet: info-0:7.1-1.fc40.aarch64
>>> Stop trigger-install scriptlet: info-0:7.1-1.fc40.aarch64
Warning: skipped PGP checks for 152 package(s).
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: alternatives-1.26-1.fc40.aarch64
ansible-srpm-macros-1-12.fc40.noarch
audit-libs-4.0-5.fc40.aarch64
authselect-1.5.0-1.fc40.aarch64
authselect-libs-1.5.0-1.fc40.aarch64
basesystem-11-18.fc39.noarch
bash-5.2.26-1.fc40.aarch64
binutils-2.41-30.fc40.aarch64
binutils-gold-2.41-30.fc40.aarch64
bzip2-1.0.8-16.fc39.aarch64
bzip2-libs-1.0.8-16.fc39.aarch64
ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch
coreutils-9.4-3.fc40.aarch64
coreutils-common-9.4-3.fc40.aarch64
cpio-2.15-1.fc40.aarch64
cracklib-2.9.11-2.fc39.aarch64
crypto-policies-20231204-1.git1e3a2e4.fc40.noarch
curl-8.5.0-2.fc40.aarch64
cyrus-sasl-lib-2.1.28-17.fc40.aarch64
debugedit-5.0-12.fc40.aarch64
diffutils-3.10-3.fc39.aarch64
dwz-0.15-3.fc39.aarch64
ed-1.20-1.fc40.aarch64
efi-srpm-macros-5-9.fc39.noarch
elfutils-0.190-4.fc40.aarch64
elfutils-debuginfod-client-0.190-4.fc40.aarch64
elfutils-default-yama-scope-0.190-4.fc40.noarch
elfutils-libelf-0.190-4.fc40.aarch64
elfutils-libs-0.190-4.fc40.aarch64
fedora-gpg-keys-40-0.2.noarch
fedora-release-40-0.29.noarch
fedora-release-common-40-0.29.noarch
fedora-release-identity-basic-40-0.29.noarch
fedora-repos-40-0.2.noarch
fedora-repos-rawhide-40-0.2.noarch
file-5.45-1.fc40.aarch64
file-libs-5.45-1.fc40.aarch64
filesystem-3.18-6.fc39.aarch64
findutils-4.9.0-6.fc40.aarch64
fonts-srpm-macros-2.0.5-12.fc39.noarch
forge-srpm-macros-0.2.0-1.fc40.noarch
fpc-srpm-macros-1.3-8.fc39.noarch
gawk-5.3.0-1.fc40.aarch64
gdb-minimal-14.1-6.fc40.aarch64
gdbm-1.23-4.fc39.aarch64
gdbm-libs-1.23-4.fc39.aarch64
ghc-srpm-macros-1.6.1-3.fc40.noarch
glibc-2.38.9000-33.fc40.aarch64
glibc-common-2.38.9000-33.fc40.aarch64
glibc-gconv-extra-2.38.9000-33.fc40.aarch64
glibc-minimal-langpack-2.38.9000-33.fc40.aarch64
gmp-6.2.1-5.fc39.aarch64
gnat-srpm-macros-6-3.fc39.noarch
go-srpm-macros-3.3.1-1.fc40.noarch
grep-3.11-5.fc40.aarch64
gzip-1.12-6.fc39.aarch64
info-7.1-1.fc40.aarch64
jansson-2.13.1-7.fc39.aarch64
kernel-srpm-macros-1.0-20.fc39.noarch
keyutils-libs-1.6.3-1.fc40.aarch64
krb5-libs-1.21.2-3.fc40.aarch64
libacl-2.3.2-1.fc40.aarch64
libarchive-3.7.2-1.fc40.aarch64
libattr-2.5.2-1.fc40.aarch64
libblkid-2.39.3-2.fc40.aarch64
libbrotli-1.1.0-1.fc40.aarch64
libcap-2.69-1.fc40.aarch64
libcap-ng-0.8.4-2.fc40.aarch64
libcom_err-1.47.0-2.fc39.aarch64
libcurl-8.5.0-2.fc40.aarch64
libeconf-0.5.2-1.fc40.aarch64
libevent-2.1.12-9.fc39.aarch64
libfdisk-2.39.3-2.fc40.aarch64
libffi-3.4.4-5.fc40.aarch64
libgcc-14.0.1-0.2.fc40.aarch64
libgomp-14.0.1-0.2.fc40.aarch64
libidn2-2.3.4-3.fc39.aarch64
libmount-2.39.3-2.fc40.aarch64
libnghttp2-1.59.0-1.fc40.aarch64
libnsl2-2.0.0-6.fc39.aarch64
libpkgconf-1.9.5-2.fc39.aarch64
libpsl-0.21.5-1.fc40.aarch64
libpwquality-1.4.5-6.fc39.aarch64
libselinux-3.6-2.fc40.aarch64
libsemanage-3.6-1.fc40.aarch64
libsepol-3.6-1.fc40.aarch64
libsmartcols-2.39.3-2.fc40.aarch64
libssh-0.10.6-2.fc40.aarch64
libssh-config-0.10.6-2.fc40.noarch
libstdc++-14.0.1-0.2.fc40.aarch64
libtasn1-4.19.0-3.fc39.aarch64
libtirpc-1.3.4-1.rc1.fc40.aarch64
libunistring-1.1-5.fc40.aarch64
libutempter-1.2.1-10.fc39.aarch64
libuuid-2.39.3-2.fc40.aarch64
libverto-0.3.2-6.fc39.aarch64
libxcrypt-4.4.36-4.fc40.aarch64
libxml2-2.12.4-1.fc40.aarch64
libzstd-1.5.5-4.fc39.aarch64
lua-libs-5.4.6-3.fc39.aarch64
lua-srpm-macros-1-9.fc39.noarch
lz4-libs-1.9.4-4.fc39.aarch64
mpfr-4.2.1-1.fc40.aarch64
ncurses-base-6.4-9.20240113.fc40.noarch
ncurses-libs-6.4-9.20240113.fc40.aarch64
ocaml-srpm-macros-9-1.fc40.noarch
openblas-srpm-macros-2-14.fc39.noarch
openldap-2.6.6-1.fc39.aarch64
openssl-libs-3.1.4-1.fc40.aarch64
p11-kit-0.25.3-1.fc40.aarch64
p11-kit-trust-0.25.3-1.fc40.aarch64
package-notes-srpm-macros-0.5-9.fc39.noarch
pam-1.6.0-1.fc40.aarch64
pam-libs-1.6.0-1.fc40.aarch64
patch-2.7.6-22.fc39.aarch64
pcre2-10.42-2.fc40.aarch64
pcre2-syntax-10.42-2.fc40.noarch
perl-srpm-macros-1-51.fc39.noarch
pkgconf-1.9.5-2.fc39.aarch64
pkgconf-m4-1.9.5-2.fc39.noarch
pkgconf-pkg-config-1.9.5-2.fc39.aarch64
popt-1.19-3.fc39.aarch64
publicsuffix-list-dafsa-20240107-1.fc40.noarch
pyproject-srpm-macros-1.11.0-1.fc40.noarch
python-srpm-macros-3.12-5.fc40.noarch
qt5-srpm-macros-5.15.12-1.fc40.noarch
qt6-srpm-macros-6.6.1-3.fc40.noarch
readline-8.2-7.fc40.aarch64
redhat-rpm-config-280-1.fc40.noarch
rpm-4.19.1-2.fc40.aarch64
rpm-build-4.19.1-2.fc40.aarch64
rpm-build-libs-4.19.1-2.fc40.aarch64
rpm-libs-4.19.1-2.fc40.aarch64
rpm-sequoia-1.5.0-2.fc40.aarch64
rust-srpm-macros-25.2-2.fc40.noarch
sed-4.8-14.fc39.aarch64
setup-2.14.5-1.fc40.noarch
shadow-utils-4.14.0-2.fc40.aarch64
sqlite-libs-3.45.0-1.fc40.aarch64
systemd-libs-255.2-2.fc40.aarch64
tar-1.35-2.fc40.aarch64
unzip-6.0-62.fc39.aarch64
util-linux-2.39.3-2.fc40.aarch64
util-linux-core-2.39.3-2.fc40.aarch64
which-2.21-40.fc39.aarch64
xxhash-libs-0.8.2-1.fc39.aarch64
xz-5.4.5-1.fc40.aarch64
xz-libs-5.4.5-1.fc40.aarch64
zig-srpm-macros-1-1.fc40.noarch
zip-3.0-39.fc40.aarch64
zlib-ng-compat-2.1.6-1.fc40.aarch64
zstd-1.5.5-4.fc39.aarch64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1706140800
Wrote: /builddir/build/SRPMS/percolator-3.06.04-3.fc40.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-aarch64-1706189148.512818/root/var/log/dnf5.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-kgpy6osc/percolator/percolator.spec) Config(child) 1 minutes 10 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-3.06.04-3.fc40.src.rpm)  Config(fedora-rawhide-aarch64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1706189148.512818/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-aarch64-bootstrap-1706189148.512818/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-aarch64-1706189148.512818/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-4.19.1-2.fc40.aarch64
  rpm-sequoia-1.5.0-2.fc40.aarch64
  python3-dnf-4.18.2-1.fc40.noarch
  yum-4.18.2-1.fc40.noarch
  dnf5-5.1.11-1.fc40.aarch64
  dnf5-plugins-5.1.11-1.fc40.aarch64
Finish: chroot init
Start: build phase for percolator-3.06.04-3.fc40.src.rpm
Start: build setup for percolator-3.06.04-3.fc40.src.rpm
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1706140800
Wrote: /builddir/build/SRPMS/percolator-3.06.04-3.fc40.src.rpm
Updating and loading repositories:
 fedora                                 100% |  81.6 KiB/s |  12.6 KiB |  00m00s
 Additional repo http_kojipkgs_fedorapr 100% | 165.0 KiB/s |   4.1 KiB |  00m00s
 Copr repository                        100% |  61.5 KiB/s |   1.5 KiB |  00m00s
Repositories loaded.
Package                    Arch    Version             Repository                                                         Size
Installing:                                                                                                                   
 boost-devel               aarch64 1.83.0-2.fc40       copr_base                                                     143.0 MiB
 boost-static              aarch64 1.83.0-2.fc40       copr_base                                                      37.0 MiB
 bzip2-devel               aarch64 1.0.8-16.fc39       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 309.8 KiB
 cmake                     aarch64 3.27.7-1.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  27.6 MiB
 gcc                       aarch64 14.0.1-0.2.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  93.0 MiB
 gcc-c++                   aarch64 14.0.1-0.2.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  34.9 MiB
 gtest-devel               aarch64 1.14.0-2.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.0 MiB
 libtirpc-devel            aarch64 1.3.4-1.rc1.fc40    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 251.5 KiB
 make                      aarch64 1:4.4.1-2.fc39      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.8 MiB
 python3-devel             aarch64 3.12.1-2.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.2 MiB
 sqlite-devel              aarch64 3.45.0-1.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 663.2 KiB
 tokyocabinet-devel        aarch64 1.4.48-23.fc39      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 460.2 KiB
 xerces-c-devel            aarch64 3.2.5-1.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   4.1 MiB
 xsd                       aarch64 4.1.0-0.12.a11.fc39 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   5.4 MiB
 zlib-ng-compat-devel      aarch64 2.1.6-1.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 103.4 KiB
Installing dependencies:                                                                                                      
 annobin-docs              noarch  12.38-1.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  95.6 KiB
 annobin-plugin-gcc        aarch64 12.38-1.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 boost                     aarch64 1.83.0-2.fc40       copr_base                                                       1.3 KiB
 boost-atomic              aarch64 1.83.0-2.fc40       copr_base                                                     196.8 KiB
 boost-chrono              aarch64 1.83.0-2.fc40       copr_base                                                     197.4 KiB
 boost-container           aarch64 1.83.0-2.fc40       copr_base                                                     197.4 KiB
 boost-context             aarch64 1.83.0-2.fc40       copr_base                                                     196.4 KiB
 boost-contract            aarch64 1.83.0-2.fc40       copr_base                                                     198.6 KiB
 boost-coroutine           aarch64 1.83.0-2.fc40       copr_base                                                     197.1 KiB
 boost-date-time           aarch64 1.83.0-2.fc40       copr_base                                                     196.3 KiB
 boost-fiber               aarch64 1.83.0-2.fc40       copr_base                                                     198.3 KiB
 boost-filesystem          aarch64 1.83.0-2.fc40       copr_base                                                     262.9 KiB
 boost-graph               aarch64 1.83.0-2.fc40       copr_base                                                     461.3 KiB
 boost-iostreams           aarch64 1.83.0-2.fc40       copr_base                                                     198.2 KiB
 boost-json                aarch64 1.83.0-2.fc40       copr_base                                                     392.1 KiB
 boost-locale              aarch64 1.83.0-2.fc40       copr_base                                                     659.2 KiB
 boost-log                 aarch64 1.83.0-2.fc40       copr_base                                                       1.7 MiB
 boost-math                aarch64 1.83.0-2.fc40       copr_base                                                       1.5 MiB
 boost-nowide              aarch64 1.83.0-2.fc40       copr_base                                                     196.9 KiB
 boost-numpy3              aarch64 1.83.0-2.fc40       copr_base                                                     197.3 KiB
 boost-program-options     aarch64 1.83.0-2.fc40       copr_base                                                     331.1 KiB
 boost-python3             aarch64 1.83.0-2.fc40       copr_base                                                     332.5 KiB
 boost-random              aarch64 1.83.0-2.fc40       copr_base                                                     197.5 KiB
 boost-regex               aarch64 1.83.0-2.fc40       copr_base                                                     330.2 KiB
 boost-serialization       aarch64 1.83.0-2.fc40       copr_base                                                     659.4 KiB
 boost-stacktrace          aarch64 1.83.0-2.fc40       copr_base                                                     587.7 KiB
 boost-system              aarch64 1.83.0-2.fc40       copr_base                                                     196.3 KiB
 boost-test                aarch64 1.83.0-2.fc40       copr_base                                                     792.3 KiB
 boost-thread              aarch64 1.83.0-2.fc40       copr_base                                                     264.3 KiB
 boost-timer               aarch64 1.83.0-2.fc40       copr_base                                                     197.0 KiB
 boost-type_erasure        aarch64 1.83.0-2.fc40       copr_base                                                     198.0 KiB
 boost-wave                aarch64 1.83.0-2.fc40       copr_base                                                     726.1 KiB
 cmake-data                noarch  3.27.7-1.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   7.8 MiB
 cmake-filesystem          aarch64 3.27.7-1.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   0.0   B
 cmake-rpm-macros          noarch  3.27.7-1.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   7.4 KiB
 cpp                       aarch64 14.0.1-0.2.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  31.7 MiB
 emacs-filesystem          noarch  1:29.2-2.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   0.0   B
 expat                     aarch64 2.5.0-3.fc39        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 526.7 KiB
 flexiblas                 aarch64 3.4.1-2.fc40        copr_base                                                      46.7 KiB
 flexiblas-netlib          aarch64 3.4.1-2.fc40        copr_base                                                       9.5 MiB
 flexiblas-openblas-openmp aarch64 3.4.1-2.fc40        copr_base                                                     195.3 KiB
 gc                        aarch64 8.2.2-4.fc39        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 850.4 KiB
 gcc-plugin-annobin        aarch64 14.0.1-0.2.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 197.0 KiB
 glibc-devel               aarch64 2.38.9000-33.fc40   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   2.2 MiB
 gmock                     aarch64 1.14.0-2.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 394.0 KiB
 gtest                     aarch64 1.14.0-2.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 718.1 KiB
 guile22                   aarch64 2.2.7-9.fc39        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  44.3 MiB
 jsoncpp                   aarch64 1.9.5-5.fc39        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 335.8 KiB
 kernel-headers            aarch64 6.8.0-0.rc1.12.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   6.1 MiB
 libasan                   aarch64 14.0.1-0.2.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.6 MiB
 libatomic                 aarch64 14.0.1-0.2.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 196.8 KiB
 libb2                     aarch64 0.98.1-9.fc39       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 202.1 KiB
 libcutl                   aarch64 1.10.0-27.fc39      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.1 MiB
 libgfortran               aarch64 14.0.1-0.2.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.5 MiB
 libicu                    aarch64 73.2-3.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  37.0 MiB
 libicu-devel              aarch64 73.2-3.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   5.7 MiB
 libmpc                    aarch64 1.3.1-3.fc39        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 280.7 KiB
 libstdc++-devel           aarch64 14.0.1-0.2.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  14.3 MiB
 libtool-ltdl              aarch64 2.4.7-10.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 222.2 KiB
 libubsan                  aarch64 14.0.1-0.2.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 539.1 KiB
 libuv                     aarch64 1:1.47.0-3.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 583.2 KiB
 libxcrypt-devel           aarch64 4.4.36-4.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  30.3 KiB
 mpdecimal                 aarch64 2.5.1-7.fc39        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 328.7 KiB
 openblas                  aarch64 0.3.26-1.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  96.0 KiB
 openblas-openmp           aarch64 0.3.26-1.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  19.3 MiB
 pyproject-rpm-macros      noarch  1.11.0-1.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  98.5 KiB
 python-pip-wheel          noarch  23.3.1-3.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.5 MiB
 python-rpm-macros         noarch  3.12-5.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  22.1 KiB
 python3                   aarch64 3.12.1-2.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 211.8 KiB
 python3-libs              aarch64 3.12.1-2.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  51.9 MiB
 python3-numpy             aarch64 1:1.26.2-4.fc40     copr_base                                                      41.6 MiB
 python3-packaging         noarch  23.2-2.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 421.1 KiB
 python3-rpm-generators    noarch  14-8.fc40           http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  82.3 KiB
 python3-rpm-macros        noarch  3.12-5.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   6.4 KiB
 rhash                     aarch64 1.4.3-3.fc39        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch 584.6 KiB
 sqlite                    aarch64 3.45.0-1.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.9 MiB
 tokyocabinet              aarch64 1.4.48-23.fc39      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   4.3 MiB
 tzdata                    noarch  2023d-2.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   1.6 MiB
 vim-filesystem            noarch  2:9.1.031-1.fc40    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  40.0   B
 xerces-c                  aarch64 3.2.5-1.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   3.6 MiB

Transaction Summary:
 Installing:       95 packages

Total size of inbound packages is 139 MiB. Need to download 139 MiB.
After this operation 659 MiB will be used (install 659 MiB, remove 0 B).
[ 1/95] bzip2-devel-0:1.0.8-16.fc39.aar 100% |   5.5 MiB/s | 213.7 KiB |  00m00s
[ 2/95] boost-static-0:1.83.0-2.fc40.aa 100% |  48.0 MiB/s |   3.4 MiB |  00m00s
[ 3/95] cmake-0:3.27.7-1.fc40.aarch64   100% |  80.0 MiB/s |   7.4 MiB |  00m00s
[ 4/95] gcc-c++-0:14.0.1-0.2.fc40.aarch 100% | 173.3 MiB/s |  12.8 MiB |  00m00s
[ 5/95] boost-devel-0:1.83.0-2.fc40.aar 100% |  52.7 MiB/s |  11.8 MiB |  00m00s
[ 6/95] gcc-0:14.0.1-0.2.fc40.aarch64   100% | 178.7 MiB/s |  33.6 MiB |  00m00s
[ 7/95] gtest-devel-0:1.14.0-2.fc40.aar 100% |   4.5 MiB/s | 242.2 KiB |  00m00s
[ 8/95] sqlite-devel-0:3.45.0-1.fc40.aa 100% |   9.7 MiB/s | 148.8 KiB |  00m00s
[ 9/95] libtirpc-devel-0:1.3.4-1.rc1.fc 100% |   6.9 MiB/s | 113.2 KiB |  00m00s
[10/95] make-1:4.4.1-2.fc39.aarch64     100% |   9.1 MiB/s | 577.5 KiB |  00m00s
[11/95] xerces-c-devel-0:3.2.5-1.fc40.a 100% |  30.3 MiB/s | 434.9 KiB |  00m00s
[12/95] tokyocabinet-devel-0:1.4.48-23. 100% |   5.4 MiB/s |  88.7 KiB |  00m00s
[13/95] python3-devel-0:3.12.1-2.fc40.a 100% |  20.6 MiB/s | 273.8 KiB |  00m00s
[14/95] zlib-ng-compat-devel-0:2.1.6-1. 100% |   5.9 MiB/s |  36.2 KiB |  00m00s
[15/95] boost-0:1.83.0-2.fc40.aarch64   100% |   7.1 MiB/s |  14.5 KiB |  00m00s
[16/95] boost-numpy3-0:1.83.0-2.fc40.aa 100% |  14.2 MiB/s |  29.1 KiB |  00m00s
[17/95] boost-atomic-0:1.83.0-2.fc40.aa 100% |   9.7 MiB/s |  19.9 KiB |  00m00s
[18/95] boost-chrono-0:1.83.0-2.fc40.aa 100% |  12.7 MiB/s |  26.0 KiB |  00m00s
[19/95] boost-container-0:1.83.0-2.fc40 100% |  19.6 MiB/s |  40.1 KiB |  00m00s
[20/95] boost-context-0:1.83.0-2.fc40.a 100% |   8.5 MiB/s |  17.5 KiB |  00m00s
[21/95] boost-contract-0:1.83.0-2.fc40. 100% |  21.6 MiB/s |  44.2 KiB |  00m00s
[22/95] boost-coroutine-0:1.83.0-2.fc40 100% |  10.3 MiB/s |  21.0 KiB |  00m00s
[23/95] boost-date-time-0:1.83.0-2.fc40 100% |  16.0 MiB/s |  16.4 KiB |  00m00s
[24/95] boost-fiber-0:1.83.0-2.fc40.aar 100% |  13.9 MiB/s |  42.7 KiB |  00m00s
[25/95] boost-filesystem-0:1.83.0-2.fc4 100% |  15.8 MiB/s |  64.7 KiB |  00m00s
[26/95] boost-iostreams-0:1.83.0-2.fc40 100% |  19.8 MiB/s |  40.6 KiB |  00m00s
[27/95] boost-json-0:1.83.0-2.fc40.aarc 100% |  34.6 MiB/s | 141.9 KiB |  00m00s
[28/95] boost-graph-0:1.83.0-2.fc40.aar 100% |  15.6 MiB/s | 143.4 KiB |  00m00s
[29/95] boost-locale-0:1.83.0-2.fc40.aa 100% |  39.3 MiB/s | 201.1 KiB |  00m00s
[30/95] boost-log-0:1.83.0-2.fc40.aarch 100% |  44.9 MiB/s | 459.4 KiB |  00m00s
[31/95] xsd-0:4.1.0-0.12.a11.fc39.aarch 100% |  24.3 MiB/s |   1.1 MiB |  00m00s
[32/95] boost-math-0:1.83.0-2.fc40.aarc 100% |  28.2 MiB/s | 259.8 KiB |  00m00s
[33/95] boost-nowide-0:1.83.0-2.fc40.aa 100% |   7.0 MiB/s |  21.4 KiB |  00m00s
[34/95] boost-random-0:1.83.0-2.fc40.aa 100% |  12.1 MiB/s |  24.8 KiB |  00m00s
[35/95] boost-python3-0:1.83.0-2.fc40.a 100% |  29.2 MiB/s |  89.6 KiB |  00m00s
[36/95] boost-program-options-0:1.83.0- 100% |  25.5 MiB/s | 104.4 KiB |  00m00s
[37/95] boost-stacktrace-0:1.83.0-2.fc4 100% |  14.7 MiB/s |  30.1 KiB |  00m00s
[38/95] boost-regex-0:1.83.0-2.fc40.aar 100% |  26.5 MiB/s | 108.7 KiB |  00m00s
[39/95] boost-serialization-0:1.83.0-2. 100% |  32.1 MiB/s | 131.6 KiB |  00m00s
[40/95] boost-system-0:1.83.0-2.fc40.aa 100% |   8.0 MiB/s |  16.3 KiB |  00m00s
[41/95] boost-timer-0:1.83.0-2.fc40.aar 100% |  10.8 MiB/s |  22.1 KiB |  00m00s
[42/95] boost-thread-0:1.83.0-2.fc40.aa 100% |  14.8 MiB/s |  60.4 KiB |  00m00s
[43/95] boost-type_erasure-0:1.83.0-2.f 100% |  10.7 MiB/s |  32.8 KiB |  00m00s
[44/95] boost-test-0:1.83.0-2.fc40.aarc 100% |  25.0 MiB/s | 230.2 KiB |  00m00s
[45/95] boost-wave-0:1.83.0-2.fc40.aarc 100% |  40.3 MiB/s | 206.6 KiB |  00m00s
[46/95] python3-0:3.12.1-2.fc40.aarch64 100% |   3.3 MiB/s |  26.8 KiB |  00m00s
[47/95] libicu-devel-0:73.2-3.fc40.aarc 100% |  39.5 MiB/s | 850.4 KiB |  00m00s
[48/95] libicu-0:73.2-3.fc40.aarch64    100% | 179.9 MiB/s |  10.4 MiB |  00m00s
[49/95] libcutl-0:1.10.0-27.fc39.aarch6 100% |  11.0 MiB/s | 292.0 KiB |  00m00s
[50/95] xerces-c-0:3.2.5-1.fc40.aarch64 100% |  86.4 MiB/s | 884.7 KiB |  00m00s
[51/95] sqlite-0:3.45.0-1.fc40.aarch64  100% |  92.8 MiB/s | 855.0 KiB |  00m00s
[52/95] tokyocabinet-0:1.4.48-23.fc39.a 100% |  21.5 MiB/s | 506.1 KiB |  00m00s
[53/95] guile22-0:2.2.7-9.fc39.aarch64  100% | 206.9 MiB/s |   6.4 MiB |  00m00s
[54/95] expat-0:2.5.0-3.fc39.aarch64    100% |  21.1 MiB/s | 108.0 KiB |  00m00s
[55/95] python3-numpy-1:1.26.2-4.fc40.a 100% |  50.2 MiB/s |   6.4 MiB |  00m00s
[56/95] python3-libs-0:3.12.1-2.fc40.aa 100% | 141.9 MiB/s |   8.8 MiB |  00m00s
[57/95] gc-0:8.2.2-4.fc39.aarch64       100% |   5.6 MiB/s | 109.6 KiB |  00m00s
[58/95] libtool-ltdl-0:2.4.7-10.fc40.aa 100% |   3.0 MiB/s |  36.3 KiB |  00m00s
[59/95] cmake-filesystem-0:3.27.7-1.fc4 100% |   3.7 MiB/s |  19.1 KiB |  00m00s
[60/95] gmock-0:1.14.0-2.fc40.aarch64   100% |   7.9 MiB/s |  56.4 KiB |  00m00s
[61/95] gtest-0:1.14.0-2.fc40.aarch64   100% |  26.5 MiB/s | 162.9 KiB |  00m00s
[62/95] libmpc-0:1.3.1-3.fc39.aarch64   100% |  17.5 MiB/s |  71.7 KiB |  00m00s
[63/95] libstdc++-devel-0:14.0.1-0.2.fc 100% | 116.5 MiB/s |   2.6 MiB |  00m00s
[64/95] glibc-devel-0:2.38.9000-33.fc40 100% |  22.5 MiB/s | 529.8 KiB |  00m00s
[65/95] cpp-0:14.0.1-0.2.fc40.aarch64   100% | 248.1 MiB/s |  10.7 MiB |  00m00s
[66/95] libasan-0:14.0.1-0.2.fc40.aarch 100% |  22.3 MiB/s | 480.6 KiB |  00m00s
[67/95] libatomic-0:14.0.1-0.2.fc40.aar 100% |   1.1 MiB/s |  21.2 KiB |  00m00s
[68/95] libubsan-0:14.0.1-0.2.fc40.aarc 100% |  17.4 MiB/s | 195.5 KiB |  00m00s
[69/95] jsoncpp-0:1.9.5-5.fc39.aarch64  100% |   8.9 MiB/s |  91.4 KiB |  00m00s
[70/95] rhash-0:1.4.3-3.fc39.aarch64    100% |  15.6 MiB/s | 191.7 KiB |  00m00s
[71/95] libuv-1:1.47.0-3.fc40.aarch64   100% |  17.3 MiB/s | 247.4 KiB |  00m00s
[72/95] cmake-data-0:3.27.7-1.fc40.noar 100% |  64.4 MiB/s |   1.7 MiB |  00m00s
[73/95] flexiblas-0:3.4.1-2.fc40.aarch6 100% |   8.2 MiB/s |  25.3 KiB |  00m00s
[74/95] flexiblas-openblas-openmp-0:3.4 100% |   8.3 MiB/s |  17.1 KiB |  00m00s
[75/95] libgfortran-0:14.0.1-0.2.fc40.a 100% |  25.1 MiB/s | 437.4 KiB |  00m00s
[76/95] openblas-openmp-0:0.3.26-1.fc40 100% | 148.2 MiB/s |   3.7 MiB |  00m00s
[77/95] libb2-0:0.98.1-9.fc39.aarch64   100% |   2.9 MiB/s |  24.1 KiB |  00m00s
[78/95] mpdecimal-0:2.5.1-7.fc39.aarch6 100% |  17.5 MiB/s |  89.6 KiB |  00m00s
[79/95] tzdata-0:2023d-2.fc40.noarch    100% |  52.9 MiB/s | 433.6 KiB |  00m00s
[80/95] python-pip-wheel-0:23.3.1-3.fc4 100% | 113.1 MiB/s |   1.5 MiB |  00m00s
[81/95] openblas-0:0.3.26-1.fc40.aarch6 100% |   7.5 MiB/s |  38.4 KiB |  00m00s
[82/95] libxcrypt-devel-0:4.4.36-4.fc40 100% |   7.1 MiB/s |  29.0 KiB |  00m00s
[83/95] kernel-headers-0:6.8.0-0.rc1.12 100% | 128.3 MiB/s |   1.4 MiB |  00m00s
[84/95] flexiblas-netlib-0:3.4.1-2.fc40 100% |  40.2 MiB/s |   2.7 MiB |  00m00s
[85/95] emacs-filesystem-1:29.2-2.fc40. 100% | 695.2 KiB/s |   7.6 KiB |  00m00s
[86/95] vim-filesystem-2:9.1.031-1.fc40 100% |   2.1 MiB/s |  17.5 KiB |  00m00s
[87/95] pyproject-rpm-macros-0:1.11.0-1 100% |   6.9 MiB/s |  42.4 KiB |  00m00s
[88/95] python3-rpm-generators-0:14-8.f 100% |   4.9 MiB/s |  30.0 KiB |  00m00s
[89/95] python-rpm-macros-0:3.12-5.fc40 100% |   2.3 MiB/s |  19.1 KiB |  00m00s
[90/95] python3-rpm-macros-0:3.12-5.fc4 100% |   1.9 MiB/s |  13.8 KiB |  00m00s
[91/95] annobin-docs-0:12.38-1.fc40.noa 100% |  17.5 MiB/s |  89.6 KiB |  00m00s
[92/95] annobin-plugin-gcc-0:12.38-1.fc 100% | 116.7 MiB/s | 956.4 KiB |  00m00s
[93/95] gcc-plugin-annobin-0:14.0.1-0.2 100% |   6.3 MiB/s |  32.5 KiB |  00m00s
[94/95] cmake-rpm-macros-0:3.27.7-1.fc4 100% |   3.6 MiB/s |  18.5 KiB |  00m00s
[95/95] python3-packaging-0:23.2-2.fc40 100% |  18.8 MiB/s | 115.5 KiB |  00m00s
--------------------------------------------------------------------------------
[95/95] Total                           100% | 207.7 MiB/s | 138.9 MiB |  00m01s
Running transaction
[ 1/97] Verify package files            100% | 187.0   B/s |  95.0   B |  00m01s
[ 2/97] Prepare transaction             100% | 482.0   B/s |  95.0   B |  00m00s
[ 3/97] Installing boost-system-0:1.83. 100% | 192.5 MiB/s | 197.1 KiB |  00m00s
[ 4/97] Installing boost-chrono-0:1.83. 100% | 193.8 MiB/s | 198.4 KiB |  00m00s
[ 5/97] Installing boost-thread-0:1.83. 100% | 259.1 MiB/s | 265.3 KiB |  00m00s
[ 6/97] Installing libicu-0:73.2-3.fc40 100% | 369.7 MiB/s |  37.0 MiB |  00m00s
[ 7/97] Installing boost-regex-0:1.83.0 100% | 161.7 MiB/s | 331.2 KiB |  00m00s
[ 8/97] Installing python-rpm-macros-0: 100% |   0.0   B/s |  22.8 KiB |  00m00s
[ 9/97] Installing libmpc-0:1.3.1-3.fc3 100% | 275.6 MiB/s | 282.2 KiB |  00m00s
[10/97] Installing cmake-filesystem-0:3 100% |   3.6 MiB/s |   7.3 KiB |  00m00s
[11/97] Installing expat-0:2.5.0-3.fc39 100% | 258.2 MiB/s | 528.8 KiB |  00m00s
[12/97] Installing boost-context-0:1.83 100% | 192.8 MiB/s | 197.4 KiB |  00m00s
[13/97] Installing boost-atomic-0:1.83. 100% | 193.2 MiB/s | 197.8 KiB |  00m00s
[14/97] Installing boost-filesystem-0:1 100% | 257.7 MiB/s | 263.9 KiB |  00m00s
[15/97] Installing python3-rpm-macros-0 100% |   0.0   B/s |   6.7 KiB |  00m00s
[16/97] Installing libgfortran-0:14.0.1 100% | 380.4 MiB/s |   1.5 MiB |  00m00s
[17/97] Installing gtest-0:1.14.0-2.fc4 100% | 351.3 MiB/s | 719.6 KiB |  00m00s
[18/97] Installing xerces-c-0:3.2.5-1.f 100% | 400.9 MiB/s |   3.6 MiB |  00m00s
[19/97] Installing boost-date-time-0:1. 100% | 192.7 MiB/s | 197.3 KiB |  00m00s
[20/97] Installing boost-container-0:1. 100% | 193.8 MiB/s | 198.4 KiB |  00m00s
[21/97] Installing boost-json-0:1.83.0- 100% | 383.9 MiB/s | 393.1 KiB |  00m00s
[22/97] Installing boost-wave-0:1.83.0- 100% | 355.0 MiB/s | 727.1 KiB |  00m00s
[23/97] Installing gmock-0:1.14.0-2.fc4 100% | 386.2 MiB/s | 395.4 KiB |  00m00s
[24/97] Installing pyproject-rpm-macros 100% |  98.1 MiB/s | 100.5 KiB |  00m00s
[25/97] Installing boost-fiber-0:1.83.0 100% | 194.7 MiB/s | 199.3 KiB |  00m00s
[26/97] Installing boost-log-0:1.83.0-2 100% | 334.9 MiB/s |   1.7 MiB |  00m00s
[27/97] Installing boost-coroutine-0:1. 100% | 193.5 MiB/s | 198.1 KiB |  00m00s
[28/97] Installing libcutl-0:1.10.0-27. 100% | 361.0 MiB/s |   1.1 MiB |  00m00s
[29/97] Installing cpp-0:14.0.1-0.2.fc4 100% | 348.0 MiB/s |  31.7 MiB |  00m00s
[30/97] Installing boost-graph-0:1.83.0 100% | 225.7 MiB/s | 462.3 KiB |  00m00s
[31/97] Installing boost-locale-0:1.83. 100% | 214.9 MiB/s | 660.2 KiB |  00m00s
[32/97] Installing libicu-devel-0:73.2- 100% | 221.7 MiB/s |   5.8 MiB |  00m00s
[33/97] Installing boost-type_erasure-0 100% | 194.4 MiB/s | 199.0 KiB |  00m00s
[34/97] Installing boost-timer-0:1.83.0 100% | 193.3 MiB/s | 198.0 KiB |  00m00s
[35/97] Installing annobin-docs-0:12.38 100% |  94.3 MiB/s |  96.6 KiB |  00m00s
[36/97] Installing vim-filesystem-2:9.1 100% |   4.6 MiB/s |   4.7 KiB |  00m00s
[37/97] Installing emacs-filesystem-1:2 100% | 531.2 KiB/s | 544.0   B |  00m00s
[38/97] Installing kernel-headers-0:6.8 100% | 160.8 MiB/s |   6.3 MiB |  00m00s
[39/97] Installing libxcrypt-devel-0:4. 100% |  15.9 MiB/s |  32.6 KiB |  00m00s
[40/97] Installing glibc-devel-0:2.38.9 100% | 124.8 MiB/s |   2.2 MiB |  00m00s
[41/97] Installing openblas-0:0.3.26-1. 100% |  95.5 MiB/s |  97.8 KiB |  00m00s
[42/97] Installing openblas-openmp-0:0. 100% | 458.8 MiB/s |  19.3 MiB |  00m00s
[43/97] Installing flexiblas-0:3.4.1-2. 100% |  46.8 MiB/s |  47.9 KiB |  00m00s
[44/97] Installing flexiblas-openblas-o 100% | 191.6 MiB/s | 196.2 KiB |  00m00s
[45/97] Installing flexiblas-netlib-0:3 100% | 328.4 MiB/s |   9.5 MiB |  00m00s
[46/97] Installing tzdata-0:2023d-2.fc4 100% |  39.0 MiB/s |   1.9 MiB |  00m00s
[47/97] Installing python-pip-wheel-0:2 100% | 506.5 MiB/s |   1.5 MiB |  00m00s
[48/97] Installing mpdecimal-0:2.5.1-7. 100% | 322.1 MiB/s | 329.9 KiB |  00m00s
[49/97] Installing libb2-0:0.98.1-9.fc3 100% |  49.6 MiB/s | 203.2 KiB |  00m00s
[50/97] Installing python3-libs-0:3.12. 100% | 305.6 MiB/s |  52.3 MiB |  00m00s
[51/97] Installing python3-0:3.12.1-2.f 100% | 208.6 MiB/s | 213.6 KiB |  00m00s
[52/97] Installing boost-python3-0:1.83 100% | 325.6 MiB/s | 333.5 KiB |  00m00s
[53/97] Installing cmake-rpm-macros-0:3 100% |   2.6 MiB/s |   8.0 KiB |  00m00s
[54/97] Installing python3-numpy-1:1.26 100% | 327.6 MiB/s |  41.9 MiB |  00m00s
[55/97] Installing boost-numpy3-0:1.83. 100% | 193.7 MiB/s | 198.3 KiB |  00m00s
[56/97] Installing python3-packaging-0: 100% | 140.6 MiB/s | 431.9 KiB |  00m00s
[57/97] Installing python3-rpm-generato 100% |  81.5 MiB/s |  83.4 KiB |  00m00s
[58/97] Installing rhash-0:1.4.3-3.fc39 100% | 192.0 MiB/s | 589.8 KiB |  00m00s
[59/97] Installing libuv-1:1.47.0-3.fc4 100% | 286.1 MiB/s | 586.0 KiB |  00m00s
[60/97] Installing jsoncpp-0:1.9.5-5.fc 100% | 329.4 MiB/s | 337.3 KiB |  00m00s
[61/97] Installing libubsan-0:14.0.1-0. 100% | 263.6 MiB/s | 539.8 KiB |  00m00s
[62/97] Installing libatomic-0:14.0.1-0 100% | 193.0 MiB/s | 197.6 KiB |  00m00s
[63/97] Installing libasan-0:14.0.1-0.2 100% | 267.1 MiB/s |   1.6 MiB |  00m00s
[64/97] Installing libstdc++-devel-0:14 100% | 277.1 MiB/s |  14.4 MiB |  00m00s
[65/97] Installing libtool-ltdl-0:2.4.7 100% | 218.0 MiB/s | 223.3 KiB |  00m00s
[66/97] Installing gc-0:8.2.2-4.fc39.aa 100% | 208.2 MiB/s | 853.0 KiB |  00m00s
[67/97] Installing guile22-0:2.2.7-9.fc 100% | 399.7 MiB/s |  44.4 MiB |  00m00s
[68/97] Installing make-1:4.4.1-2.fc39. 100% | 231.4 MiB/s |   1.9 MiB |  00m00s
[69/97] Installing gcc-0:14.0.1-0.2.fc4 100% | 367.8 MiB/s |  93.0 MiB |  00m00s
>>> Running trigger-install scriptlet: redhat-rpm-config-0:280-1.fc40.noarch
>>> Stop trigger-install scriptlet: redhat-rpm-config-0:280-1.fc40.noarch
[70/97] Installing cmake-data-0:3.27.7- 100% |  83.6 MiB/s |   8.4 MiB |  00m00s
[71/97] Installing cmake-0:3.27.7-1.fc4 100% | 406.4 MiB/s |  27.6 MiB |  00m00s
[72/97] Installing sqlite-0:3.45.0-1.fc 100% | 310.9 MiB/s |   1.9 MiB |  00m00s
[73/97] Installing tokyocabinet-0:1.4.4 100% | 396.0 MiB/s |   4.4 MiB |  00m00s
[74/97] Installing boost-test-0:1.83.0- 100% | 258.4 MiB/s | 793.8 KiB |  00m00s
[75/97] Installing boost-stacktrace-0:1 100% | 287.9 MiB/s | 589.5 KiB |  00m00s
[76/97] Installing boost-serialization- 100% | 322.7 MiB/s | 660.8 KiB |  00m00s
[77/97] Installing boost-random-0:1.83. 100% | 193.9 MiB/s | 198.5 KiB |  00m00s
[78/97] Installing boost-program-option 100% | 324.4 MiB/s | 332.1 KiB |  00m00s
[79/97] Installing boost-nowide-0:1.83. 100% | 193.2 MiB/s | 197.9 KiB |  00m00s
[80/97] Installing boost-math-0:1.83.0- 100% | 367.6 MiB/s |   1.5 MiB |  00m00s
[81/97] Installing boost-iostreams-0:1. 100% | 194.5 MiB/s | 199.2 KiB |  00m00s
[82/97] Installing boost-contract-0:1.8 100% |  97.5 MiB/s | 199.6 KiB |  00m00s
[83/97] Installing boost-0:1.83.0-2.fc4 100% |  71.6 KiB/s |   1.7 KiB |  00m00s
[84/97] Installing boost-devel-0:1.83.0 100% | 199.1 MiB/s | 145.8 MiB |  00m01s
[85/97] Installing boost-static-0:1.83. 100% | 536.5 MiB/s |  37.0 MiB |  00m00s
[86/97] Installing tokyocabinet-devel-0 100% | 226.2 MiB/s | 463.3 KiB |  00m00s
[87/97] Installing sqlite-devel-0:3.45. 100% | 324.1 MiB/s | 663.8 KiB |  00m00s
[88/97] Installing gcc-c++-0:14.0.1-0.2 100% | 360.4 MiB/s |  35.0 MiB |  00m00s
[89/97] Installing annobin-plugin-gcc-0 100% |  49.2 MiB/s |   1.1 MiB |  00m00s
>>> Running trigger-install scriptlet: redhat-rpm-config-0:280-1.fc40.noarch
>>> Stop trigger-install scriptlet: redhat-rpm-config-0:280-1.fc40.noarch
[90/97] Installing gcc-plugin-annobin-0 100% |   8.1 MiB/s | 198.6 KiB |  00m00s
>>> Running trigger-install scriptlet: redhat-rpm-config-0:280-1.fc40.noarch
>>> Stop trigger-install scriptlet: redhat-rpm-config-0:280-1.fc40.noarch
[91/97] Installing python3-devel-0:3.12 100% | 115.9 MiB/s |   1.3 MiB |  00m00s
[92/97] Installing xsd-0:4.1.0-0.12.a11 100% | 271.8 MiB/s |   5.4 MiB |  00m00s
[93/97] Installing gtest-devel-0:1.14.0 100% | 175.2 MiB/s |   1.1 MiB |  00m00s
[94/97] Installing xerces-c-devel-0:3.2 100% | 210.0 MiB/s |   4.2 MiB |  00m00s
[95/97] Installing zlib-ng-compat-devel 100% | 102.0 MiB/s | 104.5 KiB |  00m00s
[96/97] Installing libtirpc-devel-0:1.3 100% |  85.6 MiB/s | 262.9 KiB |  00m00s
[97/97] Installing bzip2-devel-0:1.0.8- 100% |   1.5 MiB/s | 310.7 KiB |  00m00s
>>> Running trigger-install scriptlet: glibc-common-0:2.38.9000-33.fc40.aarch64
>>> Stop trigger-install scriptlet: glibc-common-0:2.38.9000-33.fc40.aarch64
>>> Running trigger-install scriptlet: info-0:7.1-1.fc40.aarch64
>>> Stop trigger-install scriptlet: info-0:7.1-1.fc40.aarch64
Warning: skipped PGP checks for 95 package(s).
Finish: build setup for percolator-3.06.04-3.fc40.src.rpm
Start: rpmbuild percolator-3.06.04-3.fc40.src.rpm
Building target platforms: aarch64
Building for target aarch64
setting SOURCE_DATE_EPOCH=1706140800
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.eTjBka
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf percolator-rel-3-06-04
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/percolator-rel-3-06-04.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd percolator-rel-3-06-04
+ rm -rf /builddir/build/BUILD/percolator-rel-3-06-04-SPECPARTS
+ /usr/bin/mkdir -p /builddir/build/BUILD/percolator-rel-3-06-04-SPECPARTS
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ tar -xvf /builddir/build/SOURCES/yeast-01.sqt.tar.gz
yeast-01.shuffled2.sqt
yeast-01.shuffled.sqt
yeast-01.sqt
+ find . -type f -name '*.cpp' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.h' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.xx' -exec chmod 0644 '{}' ';'
+ find . -type f -name '*.txt' -exec chmod 0644 '{}' ';'
+ chmod a-x src/converters/MSToolkit/RAMP/README
+ mv src/converters/MSToolkit/RAMP/README src/converters/MSToolkit/RAMP/RAMP-README
+ mv src/converters/MSToolkit/RAMP/Readme.Mike.txt src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt
+ cp -p /builddir/build/SOURCES/percolator-RAMP_license_lgpl-2.1.txt RAMP_license_lgpl-2.1.txt
+ sed -e 's|./bin|bin|g' -i src/qvality/CMakeLists.txt
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.9wOfXh
+ umask 022
+ cd /builddir/build/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=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro    -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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-rel-3-06-04/percolator ~/build/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=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro    -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 14.0.1
-- The CXX compiler identification is GNU 14.0.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- CMAKE_PREFIX_PATH = ../
-- XML_SUPPORT = ON
-- GOOGLE_TEST = 
-- GOOGLE_TEST_PATH = 
-- TARGET_ARCH = aarch64
-- TOOL CHAIN FILE = 
-- PROFILING = 
-- -------------------------------------------------------------------------------
-- 
-- Architecture: 
-- Checking packages:
-- Found Xerces-C: /usr/lib64/libxerces-c.so
--               : /usr/include
--        Version: 3.2.5
-- 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 (1.9s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_SKIP_INSTALL_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR


-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-06-04/percolator
+ cd src
+ xsdcxx cxx-tree --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../../src/xml/percolator_in.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../../src/xml/percolator_out.xsd
+ cd ..
+ /usr/bin/make -O -j4 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04 -B/builddir/build/BUILD/percolator-rel-3-06-04/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/percolator//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
/usr/bin/make  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend
/usr/bin/make  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend
/usr/bin/make  -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/depend
/usr/bin/make  -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas/CMakeFiles/blas.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/build
/usr/bin/make  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[  3%] Building C object src/blas/CMakeFiles/blas.dir/daxpy.c.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/daxpy.c.o -MF CMakeFiles/blas.dir/daxpy.c.o.d -o CMakeFiles/blas.dir/daxpy.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/daxpy.c
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[  5%] Building C object src/blas/CMakeFiles/blas.dir/ddot.c.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/ddot.c.o -MF CMakeFiles/blas.dir/ddot.c.o.d -o CMakeFiles/blas.dir/ddot.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/ddot.c
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[  6%] Building C object src/blas/CMakeFiles/blas.dir/dgemv.c.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dgemv.c.o -MF CMakeFiles/blas.dir/dgemv.c.o.d -o CMakeFiles/blas.dir/dgemv.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/dgemv.c
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[  8%] Building C object src/blas/CMakeFiles/blas.dir/dnrm2.c.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dnrm2.c.o -MF CMakeFiles/blas.dir/dnrm2.c.o.d -o CMakeFiles/blas.dir/dnrm2.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/dnrm2.c
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[  9%] Building C object src/blas/CMakeFiles/blas.dir/dscal.c.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/gcc -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -O3 -Wall -Wconversion -fPIC -DNDEBUG -O3 -DNDEBUG -MD -MT src/blas/CMakeFiles/blas.dir/dscal.c.o -MF CMakeFiles/blas.dir/dscal.c.o.d -o CMakeFiles/blas.dir/dscal.c.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/blas/dscal.c
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 10%] Linking C static library libblas.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/cmake -P CMakeFiles/blas.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas && /usr/bin/cmake -E cmake_link_script CMakeFiles/blas.dir/link.txt --verbose=1
/usr/bin/ar rcv libblas.a CMakeFiles/blas.dir/daxpy.c.o CMakeFiles/blas.dir/ddot.c.o CMakeFiles/blas.dir/dgemv.c.o CMakeFiles/blas.dir/dnrm2.c.o CMakeFiles/blas.dir/dscal.c.o
a - CMakeFiles/blas.dir/daxpy.c.o
a - CMakeFiles/blas.dir/ddot.c.o
a - CMakeFiles/blas.dir/dgemv.c.o
a - CMakeFiles/blas.dir/dnrm2.c.o
a - CMakeFiles/blas.dir/dscal.c.o
/usr/bin/ranlib libblas.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 10%] Built target blas
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[  3%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Globals.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/__/Globals.cpp.o -MF CMakeFiles/picked_protein.dir/__/Globals.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 12%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Logger.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/__/Logger.cpp.o -MF CMakeFiles/picked_protein.dir/__/Logger.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 13%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/MyException.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/__/MyException.cpp.o -MF CMakeFiles/picked_protein.dir/__/MyException.cpp.o.d -o CMakeFiles/picked_protein.dir/__/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 15%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/__/Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/__/Option.cpp.o -MF CMakeFiles/picked_protein.dir/__/Option.cpp.o.d -o CMakeFiles/picked_protein.dir/__/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 16%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Database.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/Database.cpp.o -MF CMakeFiles/picked_protein.dir/Database.cpp.o.d -o CMakeFiles/picked_protein.dir/Database.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Database.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 17%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Peptide.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/Peptide.cpp.o -MF CMakeFiles/picked_protein.dir/Peptide.cpp.o.d -o CMakeFiles/picked_protein.dir/Peptide.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Peptide.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Peptide.cpp: In member function ‘PercolatorCrux::Peptide::getProteinIds()’:
/builddir/build/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-rel-3-06-04/src/picked_protein/Peptide.cpp:976:35: note: length computed here
  976 |     size_t protein_id_len = strlen(protein_id);
      |                             ~~~~~~^~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 18%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/PeptideConstraint.cpp.o -MF CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o.d -o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/PeptideConstraint.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 11%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/fido/BasicGroupBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘void BasicGroupBigraph::groupProteinsBy(const Array<Set>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:47:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   47 |   for (int k = 0; k < groups.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:58:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   58 |   for (int k = 0; k < groups.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberAssociatedProteins(int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:79:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   79 |   for (int k=0; k<s.size(); k++) {
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberActiveAssociatedProteins(int, const Array<Counter>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:90:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   90 |   for (int k=0; k<s.size(); k++) {
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityE(const Model&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  100 |   for (int k=0; k<result.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::probabilityN(const Model&, const Array<Counter>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:168:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  168 |   for (int k=0; k<n.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::logNumberOfConfigurations() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:179:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  179 |   for (int k = 0; k < originalN.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::eCorrection(const Model&, const Array<Counter>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:252:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |   for (int k=0; k<result.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityRGivenN(const Array<Counter>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:289:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  289 |   for (int k=0; k<result.size(); k++) {
      |             make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
    ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityEOverAllAlphaBeta(const GridModel&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  322 |   for ( int k=0; k<result.size(); k++) {
      |                  ~^~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp: In instantiation of ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning:    71 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning:       |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    9 |   for (int k = 0; k < rhs.size(); k++) {
      |                   ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array<T>::operator==(const Array<T>&) const [with T = int]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23:   required from ‘int HashTable<D>::searchList(const std::__cxx11::list<Node>&, const D&) const [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    44 |       if ( iter->data == data )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |            ~~~~~~~~~~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8:   required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    18 |   if ( searchList( table[index], data ) != -1 )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |        ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16:   required from ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    10 |     if ( ht.add(rhs[k]) ) {
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |          ~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    71 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  267 |   for (int k=0; k<size(); k++) {
      |                 ~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 19%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/picked_protein/PeptideSrc.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[  3%] Building CXX object src/fido/CMakeFiles/fido.dir/BasicBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/fido/BasicBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/StringTable.h:9,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:6:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘void BasicBigraph::clonePSM(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:185:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  185 |   for (int k = 0; k < s.size(); k++) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:191:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  191 |   for (int k = 0; k < s.size(); k++) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:200:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  200 |   for (int k = 0; k < associatedProteinsBySection.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:211:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  211 |     for (int j = 0; j<associatedProteinsBySection[k].size(); j++)
      |                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:217:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  217 |   for (int k = 0; k < associatedProteinsBySection.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:218:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  218 |     for (int j = 0; j < associatedProteinsBySection[k].size(); j++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘BasicBigraph BasicBigraph::buildSubgraph(const Set&, const Set&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  265 |   for (int k = 0; k < result.PSMsToProteins.associations.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:274:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  274 |   for (int k = 0; k < result.proteinsToPSMs.associations.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘int BasicBigraph::markSectionPartitions()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  384 |   for (int k = 0; k < groups.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:9:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp: In instantiation of ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:2make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
1: warning:   381 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:21: warning:       |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    9 |   for (int k = 0; k < rhs.size(); k++) {
      |                   ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array<T>::operator==(const Array<T>&) const [with T = int]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23:   required from ‘int HashTable<D>::searchList(const std::__cxx11::list<Node>&, const D&) const [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    44 |       if ( iter->data == data )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |            ~~~~~~~~~~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8:   required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    18 |   if ( searchList( table[index], data ) != -1 )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |        ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16:   required from ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    10 |     if ( ht.add(rhs[k]) ) {
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |          ~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:   381 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  267 |   for (int k=0; k<size(); k++) {
      |                 ~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[  4%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_in.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/percolator/src/percolator_in.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 22%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/Protein.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/picked_protein/Protein.cpp
In function ‘PercolatorCrux::Protein::readRawSequence(_IO_FILE*, char*, unsigned int, char*, unsigned int*)’,
    inlined from ‘PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:505:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  505 |   raw_sequence[i_seq] = '\0';
      |   ~~~~~~~~~~~~~~~~~~~~^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp: In member function ‘PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:355:15: note: at offset 40000 into destination object ‘PercolatorCrux::Protein::parseProteinFastaFile(_IO_FILE*)::buffer’ of size 40000
  355 |   static char buffer[PROTEIN_SEQUENCE_LENGTH];///> The sequence to read in.
      |               ^~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 25%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/picked_protein/ProteinPeptideIterator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 26%] Building CXX object src/CMakeFiles/perclibrary.dir/parser.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/parser.cxx.o -MF CMakeFiles/perclibrary.dir/parser.cxx.o.d -o CMakeFiles/perclibrary.dir/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx: In constructor ‘parser_impl::parser_impl()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:106:33: warning: ‘parser_impl::gp_’ will be initialized after [-Wreorder]
  106 |   std::auto_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
      |                                 ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:102:22: warning:   ‘xercesc_3_2::DOMImplementation& parser_impl::dom_impl_’ [-Wreorder]
  102 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
  144 | parser_impl::parser_impl() : clean_(true),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx: In member function ‘xsd::cxx::xml::dom::auto_ptr<xercesc_3_2::DOMDocument> parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:178:14: warning: unused variable ‘n’ [-Wunused-variable]
  178 |       size_t n(s.size());
      |              ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:170:9: warning: unused variable ‘i’ [-Wunused-variable]
  170 |     int i(1);
      |         ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 27%] Building CXX object src/CMakeFiles/perclibrary.dir/serializer.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/serializer.cxx.o -MF CMakeFiles/perclibrary.dir/serializer.cxx.o.d -o CMakeFiles/perclibrary.dir/serializer.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 20%] Building CXX object src/picked_protein/CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/picked_protein/PickedProteinCaller.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 30%] Linking CXX static library libpicked_protein.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/cmake -P CMakeFiles/picked_protein.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein && /usr/bin/cmake -E cmake_link_script CMakeFiles/picked_protein.dir/link.txt --verbose=1
/usr/bin/ar qc libpicked_protein.a CMakeFiles/picked_protein.dir/__/Globals.cpp.o CMakeFiles/picked_protein.dir/__/Logger.cpp.o CMakeFiles/picked_protein.dir/__/MyException.cpp.o CMakeFiles/picked_protein.dir/__/Option.cpp.o CMakeFiles/picked_protein.dir/Database.cpp.o CMakeFiles/picked_protein.dir/Peptide.cpp.o CMakeFiles/picked_protein.dir/PeptideConstraint.cpp.o CMakeFiles/picked_protein.dir/PeptideSrc.cpp.o CMakeFiles/picked_protein.dir/PickedProteinCaller.cpp.o CMakeFiles/picked_protein.dir/Protein.cpp.o CMakeFiles/picked_protein.dir/ProteinPeptideIterator.cpp.o
/usr/bin/ranlib libpicked_protein.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 30%] Built target picked_protein
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 31%] Building CXX object src/CMakeFiles/perclibrary.dir/MassHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/MassHandler.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 29%] Building CXX object src/CMakeFiles/perclibrary.dir/BaseSpline.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/BaseSpline.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.cpp:24:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 33%] Building CXX object src/CMakeFiles/perclibrary.dir/ResultHolder.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/ResultHolder.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 32%] Building CXX object src/CMakeFiles/perclibrary.dir/PSMDescription.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/PSMDescription.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.cpp:21:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h: In constructor ‘PSMDescription::PSMDescription()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h:126:15: warning: ‘PSMDescription::peptide’ will be initialized after [-Wreorder]
  126 |   std::string peptide;
      |               ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h:122:7: warning:   ‘int PSMDescription::specFileNr’ [-Wreorder]
  122 |   int specFileNr;
      |       ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.cpp:23:1: warning:   when initialized here [-Wreorder]
   23 | PSMDescription::PSMDescription() :
      | ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h: In constructor ‘PSMDescription::PSMDescription(const std::string&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h:126:15: warning: ‘PSMDescription::peptide’ will be initialized after [-Wreorder]
  126 |   std::string peptide;
      |               ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.h:122:7: warning:   ‘int PSMDescription::specFileNr’ [-Wreorder]
  122 |   int specFileNr;
      |       ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PSMDescription.cpp:28:1: warning:   when initialized here [-Wreorder]
   28 | PSMDescription::PSMDescription(const std::string& pep) :
      | ^~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 23%] Building CXX object src/fido/CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/fido/GroupPowerBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<double> GroupPowerBigraph::proteinProbs()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:10:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   10 |   for (int k = 0; k < subgraphs_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getGroupProtNames()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:22:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   22 |   for (int k = 0; k < subgraphs_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::printProteinWeights() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:34:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |   for (int k = 0; k < sorted.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsPercolator(std::vector<ProteinScoreHolder>&, std::map<std::__cxx11::basic_string<char>, long unsigned int>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:48:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   48 |   for (; k < sorted.size(); k++) {
      |          ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinNames(std::vector<std::vector<std::__cxx11::basic_string<char> > >&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:77:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   77 |   for (int k = 0; k < groupProtNames_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsAndNames(std::vector<std::vector<std::__cxx11::basic_string<char> > >&, std::vector<double>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:94:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   94 |   for (int k=0; k<sorted.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘double GroupPowerBigraph::getLogNumberStates() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:111:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  111 |   for (int k=0; k<subgraphs_.size(); k++) {
      |                 ~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<BasicBigraph> GroupPowerBigraph::iterativePartitionSubgraphs(BasicBigraph&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:128:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  128 |   for (int k = 0; k < preResult.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'

/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::initialize(BasicBigraph&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:188:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  188 |     for (int k = 0; k < subBasic.size(); k++) {
      |                     ~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<std::__cxx11::basic_string<char> > GroupPowerBigraph::peptideNames() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:202:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  202 |   for (int k = 0; k < subgraphs_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘std::pair<Array<Array<std::__cxx11::basic_string<char> > >, Array<double> > GroupPowerBigraph::getDescendingProteinsAndWeights() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:210:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  210 |   for (int k = 0; k < sorted.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:222:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  222 |   for (int k = 0; k < sorted.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 37%] Building CXX object src/fido/CMakeFiles/fido.dir/Numerical.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/Numerical.cpp.o -MF CMakeFiles/fido.dir/Numerical.cpp.o.d -o CMakeFiles/fido.dir/Numerical.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 38%] Building CXX object src/fido/CMakeFiles/fido.dir/Random.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/Random.cpp.o -MF CMakeFiles/fido.dir/Random.cpp.o.d -o CMakeFiles/fido.dir/Random.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp: In static member function ‘static void Random::fillRandomUniform(Array<double>&, double, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp:65:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   65 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 39%] Building CXX object src/fido/CMakeFiles/fido.dir/Set.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/fido/Set.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  142 |   for (int k=0; k<size()-1; k++) {
      |                 ~^~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 36%] Building CXX object src/CMakeFiles/perclibrary.dir/SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp: In member function ‘int SetHandler::getOptionalFields(const std::string&, std::vector<OptionalField>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp:91:27: warning: variable ‘hasRt’ set but not used [-Wunused-but-set-variable]
   91 |   bool hasScannr = false, hasRt = false, hasDm = false;
      |                           ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.cpp:91:42: warning: unused variable ‘hasDm’ [-Wunused-variable]
   91 |   bool hasScannr = false, hasRt = false, hasDm = false;
      |                                          ^~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 40%] Building CXX object src/fido/CMakeFiles/fido.dir/Vector.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/fido/Vector.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:382:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  382 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:392:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  392 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:530:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  530 |   for (int k=0; k<result.size(); k++)
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:542:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  542 |   for (int k=0; k<u.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:545:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  545 |       if ( k != u.size() - 1 )
      |            ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:559:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  559 |   for (int i=0; i<s.size(); i++)
      |                 ~^~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 43%] Linking CXX static library libfido.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido && /usr/bin/cmake -E cmake_link_script CMakeFiles/fido.dir/link.txt --verbose=1
/usr/bin/ar qc libfido.a CMakeFiles/fido.dir/BasicBigraph.cpp.o CMakeFiles/fido.dir/BasicGroupBigraph.cpp.o CMakeFiles/fido.dir/GroupPowerBigraph.cpp.o CMakeFiles/fido.dir/Numerical.cpp.o CMakeFiles/fido.dir/Random.cpp.o CMakeFiles/fido.dir/Set.cpp.o CMakeFiles/fido.dir/Vector.cpp.o
/usr/bin/ranlib libfido.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 43%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 41%] Building CXX object src/CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/StdvNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 44%] Building CXX object src/CMakeFiles/perclibrary.dir/svm.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/svm.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/svm.cpp: In function ‘svm_train’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/svm.cpp:42:38: warning: argument 1 range [18446744056529682432, 18446744073709551608] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   42 | #define Malloc(type,n) (type *)malloc((static_cast<std::size_t>(n))*sizeof(type))
      |                                ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/std_abs.h:38,
                 from /usr/include/c++/14/cmath:49,
                 from /usr/include/c++/14/math.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/svm.cpp:1:
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 34%] Building CXX object src/CMakeFiles/perclibrary.dir/XMLInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/XMLInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h:30,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h: In constructor ‘XMLInterface::XMLInterface(const std::string&, const std::string&, bool, bool, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h:119:8: warning: ‘XMLInterface::reportPepXML_’ will be initialized after [-Wreorder]
  119 |   bool reportPepXML_;
      |        ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.h:111:8: warning:   ‘bool XMLInterface::printDecoys_’ [-Wreorder]
  111 |   bool printDecoys_, printExpMass_;
      |        ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:58:1: warning:   when initialized here [-Wreorder]
   58 | XMLInterface::XMLInterface(const std::string& outputFN,
      | ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp: In member function ‘int XMLInterface::readAndScorePin(std::istream&, std::vector<double>&, Scores&, const std::string&, SetHandler&, SanityCheck*&, ProteinProbEstimator*, Enzyme*&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:258:26: warning: unused variable ‘numFeatures’ [-Wunused-variable]
  258 |       const unsigned int numFeatures = FeatureNames::getNumFeatures();
      |                          ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp: In member function ‘void XMLInterface::writePepXML_PSMs(Scores&, double, std::string)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:641:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  641 |     if (sh->q < selectionFdr_)
      |     ^~
/builddir/build/BUILD/percolator-rel-3-06-04/src/XMLInterface.cpp:643:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  643 |       index++;
      |       ^~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 47%] Building CXX object src/CMakeFiles/perclibrary.dir/Enzyme.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/Enzyme.cpp.o -MF CMakeFiles/perclibrary.dir/Enzyme.cpp.o.d -o CMakeFiles/perclibrary.dir/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 48%] Building CXX object src/CMakeFiles/perclibrary.dir/Globals.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/Globals.cpp.o -MF CMakeFiles/perclibrary.dir/Globals.cpp.o.d -o CMakeFiles/perclibrary.dir/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 50%] Building CXX object src/CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/NoNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp: In member function ‘virtual void NoNormalizer::unnormalizeweight(const std::vector<double>&, std::vector<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp:40:10: warning: unused variable ‘sum’ [-Wunused-variable]
   40 |   double sum = 0;
      |          ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp: In member function ‘virtual void NoNormalizer::normalizeweight(const std::vector<double>&, std::vector<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/NoNormalizer.cpp:49:10: warning: unused variable ‘sum’ [-Wunused-variable]
   49 |   double sum = 0;
      |          ^~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 51%] Building CXX object src/CMakeFiles/perclibrary.dir/Normalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/Normalizer.cpp.o -MF CMakeFiles/perclibrary.dir/Normalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/Normalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Normalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 46%] Building CXX object src/CMakeFiles/perclibrary.dir/CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:28,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:29:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h: In constructor ‘CrossValidation::CrossValidation(bool, bool, double, double, double, double, double, unsigned int, bool, unsigned int, bool, unsigned int, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:100:8: warning: ‘CrossValidation::trainBestPositive_’ will be initialized after [-Wreorder]
  100 |   bool trainBestPositive_;
      |        ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.h:89:16: warning:   ‘unsigned int CrossValidation::numThreads_’ [-Wreorder]
   89 |   unsigned int numThreads_;
      |                ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:32:1: warning:   when initialized here [-Wreorder]
   32 | CrossValidation::CrossValidation(bool quickValidation,
      | ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::preIterationSetup(Scores&, SanityCheck*, Normalizer*, FeatureMemoryPool&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:110:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  110 |     for (int nestedSet = 0; nestedSet < nestedXvalBins_; nestedSet++) {
      |                             ~~~~~~~~~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::doStep(Normalizer*, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:296:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<candidateCposCfrac>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  296 |    for (int pairIdx = 0; pairIdx < classWeightsPerFold_.size(); pairIdx++){
      |                          ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp: In member function ‘int CrossValidation::mergeCpCnPairs(double, options&, std::vector<std::vector<Scores> >&, const std::vector<double>&, const std::vector<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:370:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  370 |   for (set = 0; set < numFolds_; ++set) {
      |                 ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:410:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  410 |     for (set = 0; set < numFolds_; ++set) {
      |                   ~~~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/CrossValidation.cpp:441:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  441 |   for (set = 0; set < numFolds_; ++set) {
      |                 ~~~~^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 24%] Building CXX object src/CMakeFiles/perclibrary.dir/percolator_out.cxx.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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_out.cxx.o -MF CMakeFiles/perclibrary.dir/percolator_out.cxx.o.d -o CMakeFiles/perclibrary.dir/percolator_out.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/percolator_out.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 53%] Building CXX object src/CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/UniNormalizer.cpp.o -MF CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o.d -o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/UniNormalizer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 52%] Building CXX object src/CMakeFiles/perclibrary.dir/SanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/SanityCheck.cpp.o -MF CMakeFiles/perclibrary.dir/SanityCheck.cpp.o.d -o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp:21:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp:24:
/builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.h: In constructor ‘SanityCheck::SanityCheck()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.h:87:8: warning: ‘SanityCheck::concatenatedSearch_’ will be initialized after [-Wreorder]
   87 |   bool concatenatedSearch_;
      |        ^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.h:72:10: warning:   ‘double SanityCheck::test_fdr_’ [-Wreorder]
   72 |   double test_fdr_, initial_train_fdr_;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/SanityCheck.cpp:31:1: warning:   when initialized here [-Wreorder]
   31 | SanityCheck::SanityCheck() :
      | ^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 55%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureNames.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/FeatureNames.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 56%] Building CXX object src/CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/LogisticRegression.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.cpp:27:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 54%] Building CXX object src/CMakeFiles/perclibrary.dir/DataSet.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/DataSet.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 58%] Building CXX object src/CMakeFiles/perclibrary.dir/Option.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 45%] Building CXX object src/CMakeFiles/perclibrary.dir/Caller.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/Caller.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h: In constructor ‘Caller::Caller()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:111:27: warning: ‘Caller::analytics_’ will be initialized after [-Wreorder]
  111 |     skipNormalizeScores_, analytics_;
      |                           ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:97:8: warning:   ‘bool Caller::xmlPrintDecoys_’ [-Wreorder]
   97 |   bool xmlPrintDecoys_, xmlPrintExpMass_;
      |        ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp:36:1: warning:   when initialized here [-Wreorder]
   36 | Caller::Caller() :
      | ^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:110:48: warning: ‘Caller::trainBestPositive_’ will be initialized after [-Wreorder]
  110 |   bool reportEachIteration_, quickValidation_, trainBestPositive_,
      |                                                ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:108:59: warning:   ‘unsigned int Caller::numThreads_’ [-Wreorder]
  108 |   unsigned int numIterations_, maxPSMs_, nestedXvalBins_, numThreads_;
      |                                                           ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.cpp:36:1: warning:   when initialized here [-Wreorder]
   36 | Caller::Caller() :
      | ^~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 61%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/ProteinFDRestimator.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 63%] Building CXX object src/CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/PseudoRandom.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 65%] Building CXX object src/CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/SqtSanityCheck.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SqtSanityCheck.cpp:17:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 60%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/ProteinProbEstimator.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h: In constructor ‘ProteinProbEstimator::ProteinProbEstimator(bool, double, bool, std::string, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:238:16: warning: ‘ProteinProbEstimator::absenceRatio_’ will be initialized after [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |                ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:238:10: warning:   ‘double ProteinProbEstimator::pi0_’ [-Wreorder]
  238 |   double pi0_, absenceRatio_;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:242:16: warning: ‘ProteinProbEstimator::numberTargetProteins_’ will be initialized after [-Wreorder]
  242 |   unsigned int numberTargetProteins_;
      |                ^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:237:8: warning:   ‘bool ProteinProbEstimator::usePi0_’ [-Wreorder]
  237 |   bool usePi0_;
      |        ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:243:15: warning: ‘ProteinProbEstimator::decoyPattern_’ will be initialized after [-Wreorder]
  243 |   std::string decoyPattern_;
      |               ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:240:10: warning:   ‘double ProteinProbEstimator::fdr_’ [-Wreorder]
  240 |   double fdr_;
      |          ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.cpp:25:1: warning:   when initialized here [-Wreorder]
   25 | ProteinProbEstimator::ProteinProbEstimator(bool trivialGrouping, double absenceRatio,
      | ^~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 67%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedVector.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/PackedVector.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.cpp:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 66%] Building CXX object src/CMakeFiles/perclibrary.dir/ssl.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/ssl.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 68%] Building CXX object src/CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/PackedMatrix.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedMatrix.h:11,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedMatrix.cpp:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 70%] Building CXX object src/CMakeFiles/perclibrary.dir/Logger.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/Logger.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 59%] Building CXX object src/CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/PosteriorEstimator.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.cpp:37:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 72%] Building CXX object src/CMakeFiles/perclibrary.dir/MyException.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/MyException.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 74%] Building CXX object src/CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/ProteinScoreHolder.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.h: In constructor ‘ProteinScoreHolder::ProteinScoreHolder(std::string, bool, Peptide, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.h:108:8: warning: ‘ProteinScoreHolder::isDecoy_’ will be initialized after [-Wreorder]
  108 |   bool isDecoy_;
      |        ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.h:106:7: warning:   ‘int ProteinScoreHolder::groupId_’ [-Wreorder]
  106 |   int groupId_;
      |       ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinScoreHolder.cpp:20:1: warning:   when initialized here [-Wreorder]
   20 | ProteinScoreHolder::ProteinScoreHolder(std::string name, bool isDecoy, ProteinScoreHolder::Peptide peptide,
      | ^~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 69%] Building CXX object src/CMakeFiles/perclibrary.dir/Matrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/Matrix.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp: In member function ‘const Matrix& Matrix::operator=(const Array<Array<double> >&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp:10:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   10 |   for (int k=0; k<rhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp: In function ‘Array<Array<double> > operator-(const Array<Array<double> >&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Matrix.cpp:519:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  519 |   for (int k=0; k<result.size(); k++)
      |                 ~^~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 76%] Building CXX object src/CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/FeatureMemoryPool.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 73%] Building CXX object src/CMakeFiles/perclibrary.dir/FidoInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/FidoInterface.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.h:20,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.h: In constructor ‘FidoInterface::FidoInterface(double, double, double, bool, bool, bool, unsigned int, double, double, double, double, bool, std::string, bool, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.h:110:10: warning: ‘FidoInterface::mseThreshold_’ will be initialized after [-Wreorder]
  110 |   double mseThreshold_;
      |          ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.h:106:8: warning:   ‘bool FidoInterface::doGridSearch_’ [-Wreorder]
  106 |   bool doGridSearch_;
      |        ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.cpp:76:1: warning:   when initialized here [-Wreorder]
   76 | FidoInterface::FidoInterface(double alpha, double beta, double gamma,
      | ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.cpp: In member function ‘double FidoInterface::estimatePriors(Scores&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/FidoInterface.cpp:132:10: warning: variable ‘prior’ set but not used [-Wunused-but-set-variable]
  132 |   double prior, prior2, prior3, prior4;
      |          ^~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 79%] Building CXX object src/CMakeFiles/perclibrary.dir/Timer.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/Timer.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 80%] Building CXX object src/CMakeFiles/perclibrary.dir/TmpDir.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/TmpDir.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 81%] Building CXX object src/CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/ValidateTabFile.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ValidateTabFile.h:6,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ValidateTabFile.cpp:1:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 77%] Building CXX object src/CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/GoogleAnalytics.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 75%] Building CXX object src/CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/PickedProteinInterface.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:27,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:34:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h: In constructor ‘PickedProteinInterface::PickedProteinInterface(const std::string&, double, bool, bool, bool, double, bool, std::string&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:86:10: warning: ‘PickedProteinInterface::maxPeptidePval_’ will be initialized after [-Wreorder]
   86 |   double maxPeptidePval_;
      |          ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:85:8: warning:   ‘bool PickedProteinInterface::reportFragmentProteins_’ [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |        ^~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:85:33: warning: ‘PickedProteinInterface::reportDuplicateProteins_’ will be initialized after [-Wreorder]
   85 |   bool reportFragmentProteins_, reportDuplicateProteins_;
      |                                 ^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.h:83:26: warning:   ‘ProteinInferenceMethod PickedProteinInterface::protInferenceMethod_’ [-Wreorder]
   83 |   ProteinInferenceMethod protInferenceMethod_;
      |                          ^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:22:1: warning:   when initialized here [-Wreorder]
   22 | PickedProteinInterface::PickedProteinInterface(const std::string& fastaDatabase,
      | ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp: In member function ‘virtual bool PickedProteinInterface::initialize(Scores&, const Enzyme*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/PickedProteinInterface.cpp:165:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  165 |     if (total_non_enzymatic_flanks > peptideScores.size()) {
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 62%] Building CXX object src/CMakeFiles/perclibrary.dir/Scores.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/Scores.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp:35:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp: In member function ‘void ScoreHolder::printPepXML(std::ostream&, std::map<char, float>&, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp:163:16: warning: unused variable ‘native_id’ [-Wunused-variable]
  163 |   unsigned int native_id = scan - 1;
      |                ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.cpp:167:10: warning: unused variable ‘RT’ [-Wunused-variable]
  167 |   double RT = pPSM->getRetentionTime();
      |          ^~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 82%] Linking CXX static library libperclibrary.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/cmake -P CMakeFiles/perclibrary.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary.dir/link.txt --verbose=1
/usr/bin/ar qc libperclibrary.a CMakeFiles/perclibrary.dir/percolator_in.cxx.o CMakeFiles/perclibrary.dir/percolator_out.cxx.o CMakeFiles/perclibrary.dir/parser.cxx.o CMakeFiles/perclibrary.dir/serializer.cxx.o CMakeFiles/perclibrary.dir/BaseSpline.cpp.o CMakeFiles/perclibrary.dir/MassHandler.cpp.o CMakeFiles/perclibrary.dir/PSMDescription.cpp.o CMakeFiles/perclibrary.dir/ResultHolder.cpp.o CMakeFiles/perclibrary.dir/XMLInterface.cpp.o CMakeFiles/perclibrary.dir/SetHandler.cpp.o CMakeFiles/perclibrary.dir/StdvNormalizer.cpp.o CMakeFiles/perclibrary.dir/svm.cpp.o CMakeFiles/perclibrary.dir/Caller.cpp.o CMakeFiles/perclibrary.dir/CrossValidation.cpp.o CMakeFiles/perclibrary.dir/Enzyme.cpp.o CMakeFiles/perclibrary.dir/Globals.cpp.o CMakeFiles/perclibrary.dir/NoNormalizer.cpp.o CMakeFiles/perclibrary.dir/Normalizer.cpp.o CMakeFiles/perclibrary.dir/SanityCheck.cpp.o CMakeFiles/perclibrary.dir/UniNormalizer.cpp.o CMakeFiles/perclibrary.dir/DataSet.cpp.o CMakeFiles/perclibrary.dir/FeatureNames.cpp.o CMakeFiles/perclibrary.dir/LogisticRegression.cpp.o CMakeFiles/perclibrary.dir/Option.cpp.o CMakeFiles/perclibrary.dir/PosteriorEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinProbEstimator.cpp.o CMakeFiles/perclibrary.dir/ProteinFDRestimator.cpp.o CMakeFiles/perclibrary.dir/Scores.cpp.o CMakeFiles/perclibrary.dir/PseudoRandom.cpp.o CMakeFiles/perclibrary.dir/SqtSanityCheck.cpp.o CMakeFiles/perclibrary.dir/ssl.cpp.o CMakeFiles/perclibrary.dir/PackedVector.cpp.o CMakeFiles/perclibrary.dir/PackedMatrix.cpp.o CMakeFiles/perclibrary.dir/Matrix.cpp.o CMakeFiles/perclibrary.dir/Logger.cpp.o CMakeFiles/perclibrary.dir/MyException.cpp.o CMakeFiles/perclibrary.dir/FidoInterface.cpp.o CMakeFiles/perclibrary.dir/ProteinScoreHolder.cpp.o CMakeFiles/perclibrary.dir/PickedProteinInterface.cpp.o CMakeFiles/perclibrary.dir/FeatureMemoryPool.cpp.o CMakeFiles/perclibrary.dir/GoogleAnalytics.cpp.o CMakeFiles/perclibrary.dir/Timer.cpp.o CMakeFiles/perclibrary.dir/TmpDir.cpp.o CMakeFiles/perclibrary.dir/ValidateTabFile.cpp.o
/usr/bin/ranlib libperclibrary.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 84%] Built target perclibrary
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend
/usr/bin/make  -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/depend
/usr/bin/make  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build
/usr/bin/make  -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 87%] Building CXX object src/qvality/CMakeFiles/qvality.dir/qvality_main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/qvality/qvality_main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/./PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/./BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/./LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/./PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/qvality/qvality_main.cpp:20:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 88%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/tests/unit_tests/percolator/Unit_tests_Percolator_main.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/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-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 89%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Fido.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Fido.cpp:24:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 86%] Building CXX object src/CMakeFiles/percolator.dir/main.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/. -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/main.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/Caller.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/main.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 93%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_TabReader.cpp:23:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 94%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:20:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp: In member function ‘int SetHandlerTest::testInput(SetHandler*, const char*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_SetHandler.cpp:65:8: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else]
   65 |     if (n > 0)
      |        ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 96%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_DataSet.cpp:23:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 98%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:19:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp: In member function ‘virtual void CrossValidationTest_doStepTest_Test::TestBody()’:
/builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_CrossValidation.cpp:140:9: warning: unused variable ‘numInit’ [-Wunused-variable]
  140 |     int numInit = crossValidation->preIterationSetup(scores, pCheck, pNorm,
      |         ^~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 90%] Linking CXX executable qvality
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality && /usr/bin/cmake -E cmake_link_script CMakeFiles/qvality.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro    -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc -rdynamic CMakeFiles/qvality.dir/qvality_main.cpp.o -o qvality   -L/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src  ../libperclibrary.a ../fido/libfido.a 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 98%] Built target qvality
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 97%] Building CXX object tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DGTEST_LINKED_AS_SHARED_LIBRARY=1 -DXML_SUPPORT -I/builddir/build/BUILD/percolator-rel-3-06-04/src -I/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -I/builddir/build/BUILD/percolator-rel-3-06-04/percolator/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/SetHandler.h:36,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator/UnitTest_Percolator_Scores.cpp:24:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PackedVector.h:14,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/BaseSpline.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/LogisticRegression.h:23,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/PosteriorEstimator.h:25,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/ProteinProbEstimator.h:33,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/DataSet.h:39:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 95%] Linking CXX executable percolator
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/percolator.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro    -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc -rdynamic CMakeFiles/percolator.dir/main.cpp.o -o percolator  libperclibrary.a blas/libblas.a fido/libfido.a picked_protein/libpicked_protein.a -lxerces-c -ltirpc -lstdc++ /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_system.a /usr/lib64/libboost_atomic.a 
In function ‘readRawSequence’,
    inlined from ‘parseProteinFastaFile’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:366:23:
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:505:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
  505 |   raw_sequence[i_seq] = '\0';
      |                       ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp: In member function ‘parseProteinFastaFile’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein/Protein.cpp:355:15: note: at offset 40000 into destination object ‘buffer’ of size 40000
  355 |   static char buffer[PROTEIN_SEQUENCE_LENGTH];///> The sequence to read in.
      |               ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[100%] Built target percolator
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[100%] Linking CXX executable gtest_unit
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest_unit.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro    -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc -rdynamic CMakeFiles/gtest_unit.dir/Unit_tests_Percolator_main.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Fido.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Option.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_TabReader.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_SetHandler.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_DataSet.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_Scores.cpp.o CMakeFiles/gtest_unit.dir/UnitTest_Percolator_CrossValidation.cpp.o -o gtest_unit  ../../../src/libperclibrary.a ../../../src/blas/libblas.a ../../../src/fido/libfido.a -lpthread /usr/lib64/libgtest_main.so.1.14.0 /usr/lib64/libgtest.so.1.14.0 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[100%] Built target gtest_unit
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ mkdir -p fido
+ pushd fido
~/build/BUILD/percolator-rel-3-06-04/fido ~/build/BUILD/percolator-rel-3-06-04
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro    -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 14.0.1
-- The CXX compiler identification is GNU 14.0.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done (0.8s)
-- 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-rel-3-06-04/fido
+ /usr/bin/make -O -j4 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04/src/fido -B/builddir/build/BUILD/percolator-rel-3-06-04/fido --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/fido/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/fido//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
/usr/bin/make  -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
cd /builddir/build/BUILD/percolator-rel-3-06-04/fido && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/fido /builddir/build/BUILD/percolator-rel-3-06-04/fido /builddir/build/BUILD/percolator-rel-3-06-04/fido/CMakeFiles/fido.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
/usr/bin/make  -f CMakeFiles/fido.dir/build.make CMakeFiles/fido.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 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-rel-3-06-04/src/fido/Numerical.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 62%] Building CXX object CMakeFiles/fido.dir/Random.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/fido/Random.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp: In static member function ‘static void Random::fillRandomUniform(Array<double>&, double, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Random.cpp:65:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   65 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 75%] Building CXX object CMakeFiles/fido.dir/Set.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/fido/Set.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp: In member function ‘bool Set::verify() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.cpp:142:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  142 |   for (int k=0; k<size()-1; k++) {
      |                 ~^~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 87%] Building CXX object CMakeFiles/fido.dir/Vector.o
/usr/bin/g++  -I/src -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/fido/Vector.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double operator*(const Array<double>&, const Array<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:382:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  382 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘const Array<double>& operator*=(Array<double>&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:392:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  392 |   for (int k=0; k<lhs.size(); k++)
      |                 ~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘Array<double> operator-(const Array<double>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:530:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  530 |   for (int k=0; k<result.size(); k++)
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In member function ‘void Vector::displayVector() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:542:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  542 |   for (int k=0; k<u.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:545:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  545 |       if ( k != u.size() - 1 )
      |            ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp: In function ‘double diffNormSquared(const Vector&, const Vector&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.cpp:559:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  559 |   for (int i=0; i<s.size(); i++)
      |                 ~^~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 50%] 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-rel-3-06-04/src/fido/BasicGroupBigraph.cpp
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
../src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
../src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:84:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
   84 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
                 from /usr/include/c++/14/bits/locale_classes.h:40,
                 from /usr/include/c++/14/bits/ios_base.h:41,
                 from /usr/include/c++/14/ios:44,
                 from /usr/include/c++/14/ostream:40,
                 from /usr/include/c++/14/iostream:41,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:11:
/usr/include/c++/14/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++/14/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++/14/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++/14/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++/14/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++/14/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++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘void BasicGroupBigraph::groupProteinsBy(const Array<Set>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:47:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   47 |   for (int k = 0; k < groups.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:58:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   58 |   for (int k = 0; k < groups.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGromake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
upBigraph::numberAssociatedProteins(int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:79:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   79 |   for (int k=0; k<s.size(); k++) {
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘int BasicGroupBigraph::numberActiveAssociatedProteins(int, const Array<Counter>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:90:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   90 |   for (int k=0; k<s.size(); k++) {
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityE(const Model&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  100 |   for (int k=0; k<result.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::probabilityN(const Model&, const Array<Counter>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:168:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  168 |   for (int k=0; k<n.size(); k++)
      |                 ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘double BasicGroupBigraph::logNumberOfConfigurations() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:179:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  179 |   for (int k = 0; k < originalN.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::eCorrection(const Model&, const Array<Counter>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:252:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  252 |   for (int k=0; k<result.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityRGivenN(const Array<Counter>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:289:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  289 |   for (int k=0; k<result.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp: In member function ‘Array<double> BasicGroupBigraph::probabilityEOverAllAlphaBeta(const GridModel&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  322 |   for ( int k=0; k<result.size(); k++) {
      |                  ~^~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp: In instantiation of ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning:    71 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:322:19: warning:       |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    9 |   for (int k = 0; k < rhs.size(); k++) {
      |                   ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array<T>::operator==(const Array<T>&) const [with T = int]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23:   required from ‘int HashTable<D>::searchList(const std::__cxx11::list<Node>&, const D&) const [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    44 |       if ( iter->data == data )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |            ~~~~~~~~~~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8:   required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    18 |   if ( searchList( table[index], data ) != -1 )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |        ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16:   required from ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    10 |     if ( ht.add(rhs[k]) ) {
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |          ~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.cpp:71:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    71 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  267 |   for (int k=0; k<size(); k++) {
      |                 ~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 50%] Building CXX object CMakeFiles/fido.dir/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-rel-3-06-04/src/fido/GroupPowerBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:4:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicGroupBigraph.h:8:
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
../src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
../src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:84:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
   84 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
                 from /usr/include/c++/14/bits/locale_classes.h:40,
                 from /usr/include/c++/14/bits/ios_base.h:41,
                 from /usr/include/c++/14/ios:44,
                 from /usr/include/c++/14/ostream:40,
                 from /usr/include/c++/14/iostream:41,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:11:
/usr/include/c++/14/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++/14/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++/14/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++/14/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++/14/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++/14/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++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<double> GroupPowerBigraph::proteinProbs()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:10:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   10 |   for (int k = 0; k < subgraphs_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getGroupProtNames()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:22:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   22 |   for (int k = 0; k < subgraphs_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::printProteinWeights() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:34:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   34 |   for (int k = 0; k < sorted.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsPercolator(std::vector<ProteinScoreHolder>&, std::map<std::__cxx11::basic_string<char>, long unsigned int>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:48:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   48 |   for (; k < sorted.size(); k++) {
      |          ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinNames(std::vector<std::vector<std::__cxx11::basic_string<char> > >&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:77:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   77 |   for (int k = 0; k < groupProtNames_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::getProteinProbsAndNames(std::vector<std::vector<std::__cxx11::basic_string<char> > >&, std::vector<double>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:94:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   94 |   for (int k=0; k<sorted.size(); k++) {
      |                 ~^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘double GroupPowerBigraph::getLogNumberStates() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:111:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  111 |   for (int k=0; k<subgraphs_.size(); k++) {
      |                 ~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<BasicBigraph> GroupPowerBigraph::iterativePartitionSubgraphs(BasicBigraph&, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:128:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  128 |   for (int k = 0; k < preResult.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘void GroupPowerBigraph::initialize(BasicBigraph&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:188:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  188 |     for (int k = 0; k < subBasic.size(); k++) {
      |                     ~~^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘Array<std::__cxx11::basic_string<char> > GroupPowerBigraph::peptideNames() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:202:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  202 |   for (int k = 0; k < subgraphs_.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp: In member function ‘std::pair<Array<Array<std::__cxx11::basic_string<char> > >, Array<double> > GroupPowerBigraph::getDescendingProteinsAndWeights() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:210:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  210 |   for (int k = 0; k < sorted.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/GroupPowerBigraph.cpp:222:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  222 |   for (int k = 0; k < sorted.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[ 50%] 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-rel-3-06-04/src/fido/BasicBigraph.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:5,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:4:
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder()’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
../src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:56:3: warning:   when initialized here [-Wreorder]
   56 |   ScoreHolder() : score(0.0), q(0.0), pep(0.0), p(0.0), label(0), pPSM(NULL) {}
      |   ^~~~~~~~~~~
../src/Scores.h: In constructor ‘ScoreHolder::ScoreHolder(double, int, PSMDescription*)’:
../src/Scores.h:54:7: warning: ‘ScoreHolder::label’ will be initialized after [-Wreorder]
   54 |   int label;
      |       ^~~~~
../src/Scores.h:53:19: warning:   ‘PSMDescription* ScoreHolder::pPSM’ [-Wreorder]
   53 |   PSMDescription* pPSM;
      |                   ^~~~
../src/Scores.h:57:3: warning:   when initialized here [-Wreorder]
   57 |   ScoreHolder(const double s, const int l, PSMDescription* psm = NULL) :
      |   ^~~~~~~~~~~
../src/Scores.h: At global scope:
../src/Scores.h:84:32: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
   84 | struct lexicOrderProb : public binary_function<ScoreHolder, ScoreHolder, bool> {
      |                                ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
                 from /usr/include/c++/14/bits/locale_classes.h:40,
                 from /usr/include/c++/14/bits/ios_base.h:41,
                 from /usr/include/c++/14/ios:44,
                 from /usr/include/c++/14/istream:40,
                 from /usr/include/c++/14/fstream:40,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:4:
/usr/include/c++/14/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++/14/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++/14/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++/14/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++/14/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++/14/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++/14/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.h:147,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/StringTable.h:9,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:6:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:139:10: warning: ‘Array<T> Array<T>::operator[](const Array<int>&) const [with T = int]’ was hidden [-Woverloaded-virtual=]
  139 | Array<T> Array<T>::operator [](const Array<int> & rhs) const
      |          ^~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Vector.h:7,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:8:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:52:5: warning: ‘T& Array<T>::operator[](std::size_t) [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   52 | T & Array<T>::operator [] (std::size_t k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:45:11: warning: ‘const T& Array<T>::operator[](std::size_t) const [with T = int; std::size_t = long unsigned int]’ was hidden [-Woverloaded-virtual=]
   45 | const T & Array<T>::operator [] (std::size_t k) const
      |           ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:38:5: warning: ‘T& Array<T>::operator[](int) [with T = int]’ was hidden [-Woverloaded-virtual=]
   38 | T & Array<T>::operator [] (int k)
      |     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Set.h:31:15: note:   by ‘Set::operator[]’
   31 |   const int & operator [](int k) const {
      |               ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘void BasicBigraph::clonePSM(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:185:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  185 |   for (int k = 0; k < s.size(); k++) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:191:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  191 |   for (int k = 0; k < s.size(); k++) {
      |                   ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:200:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  200 |   for (int k = 0; k < associatedProteinsBySection.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:211:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  211 |     for (int j = 0; j<associatedProteinsBySection[k].size(); j++)
      |                     ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:217:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  217 |   for (int k = 0; k < associatedProteinsBySection.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:218:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  218 |     for (int j = 0; j < associatedProteinsBySection[k].size(); j++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘BasicBigraph BasicBigraph::buildSubgraph(const Set&, const Set&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:265:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  265 |   for (int k = 0; k < result.PSMsToProteins.associations.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:274:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  274 |   for (int k = 0; k < result.proteinsToPSMs.associations.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp: In member function ‘int BasicBigraph::markSectionPartitions()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  384 |   for (int k = 0; k < groups.size(); k++) {
      |                   ~~^~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.h:17,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.h:9:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp: In instantiation of ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:21: warning:   381 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:384:21: warning:       |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    9 |   for (int k = 0; k < rhs.size(); k++) {
      |                   ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp: In instantiation of ‘bool Array<T>::operator==(const Array<T>&) const [with T = int]’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:44:23:   required from ‘int HashTable<D>::searchList(const std::__cxx11::list<Node>&, const D&) const [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    44 |       if ( iter->data == data )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |            ~~~~~~~~~~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/HashTable.cpp:18:8:   required from ‘bool HashTable<D>::add(const D&) [with D = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    18 |   if ( searchList( table[index], data ) != -1 )
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |        ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:10:16:   required from ‘static Array<Set> ReplicateIndexer<T>::replicates(unsigned int (*)(const T&), const Array<T>&) [with T = Set]’
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:    10 |     if ( ht.add(rhs[k]) ) {
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |          ~~~~~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/BasicBigraph.cpp:381:56:   required from here
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:   381 |   Array<Set> groups = ReplicateIndexer<Set>::replicates(Set::sumSetElements, proteinsToPSMs.associations );
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/ReplicateIndexer.cpp:9:21: warning:       |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/fido/Array.cpp:267:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  267 |   for (int k=0; k<size(); k++) {
      |                 ~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[100%] Linking CXX static library libfido.a
/usr/bin/cmake -P CMakeFiles/fido.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/fido.dir/link.txt --verbose=1
/usr/bin/ar qc libfido.a CMakeFiles/fido.dir/BasicBigraph.o CMakeFiles/fido.dir/BasicGroupBigraph.o CMakeFiles/fido.dir/GroupPowerBigraph.o CMakeFiles/fido.dir/Numerical.o CMakeFiles/fido.dir/Random.o CMakeFiles/fido.dir/Set.o CMakeFiles/fido.dir/Vector.o
/usr/bin/ranlib libfido.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
[100%] Built target fido
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/fido'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/fido/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ mkdir -p converters
+ pushd converters
~/build/BUILD/percolator-rel-3-06-04/converters ~/build/BUILD/percolator-rel-3-06-04
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro    -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 14.0.1
-- The CXX compiler identification is GNU 14.0.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- 
-- -------------------------------------------------------------------------------
-- Building PERCOLATOR-CONVERTERS:
-- change a configuration variable with: cmake -D<Variable>=<Value>
-- Indicate the type of XML serialization scheme :
		  -DSERIALIZE="Boost" or -DSERIALIZE="TokyoCabinet"
		  or -DSERIALIZE="LevelDB".
		  By setting up the variable SERIALIZE to either Boost
		  or TokyoCabinet or LevelDB you will choose the serialization
		  scheme that will be used to build Converters.
		  Boost serialization option will be used as default if no option is given.
-- CMAKE_INSTALL_PREFIX = /usr
-- CMAKE_BUILD_TYPE = Release
-- XML_SUPPORT = ON
-- PERCOLATOR_SOURCE_DIR = /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../..
-- CMAKE_PREFIX_PATH = ../
-- TARGET_ARCH = 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: 3.2.5
-- Package CodeSynthesis XSD found: /usr/include
--                      Executable: /usr/bin/xsdcxx
-- Found TokyoCabinet: /usr/lib64/libtokyocabinet.so  
-- Package Tokyo Cabinet found : /usr/include
-- Found BZip2: /usr/lib64/libbz2.so  
-- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so
-- Looking for BZ2_bzCompressInit in /usr/lib64/libbz2.so - found
-- Bzip2 found
-- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.46.0") found components: filesystem system 
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE  
-- RPC found, will include headers from: /usr/include/tirpc
-- and libraries from                  : /usr/lib64/libtirpc.so
-- Generating classes from xsd-schema using CodeSynthesis
-- Generating /builddir/build/BUILD/percolator-rel-3-06-04/converters/gaml_tandem1.0.cxx;/builddir/build/BUILD/percolator-rel-3-06-04/converters/gaml_tandem1.0.hxx
-- SQL Lite 3 found: /usr/include
-- Found ZLIB: /usr/lib64/libz.so (found version "1.3.0")  
-- ZLIB found: /usr/include, /usr/lib64/libz.so
-- Using FragSpectrumScanDatabaseTokyodb.cpp
-- Configuring done (2.2s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_Fortran_FLAGS_RELEASE
    CMAKE_INSTALL_DO_STRIP
    CMAKE_SKIP_INSTALL_RPATH
    INCLUDE_INSTALL_DIR
    LIB_INSTALL_DIR
    LIB_SUFFIX
    SHARE_INSTALL_PREFIX
    SYSCONF_INSTALL_DIR


-- Build files have been written to: /builddir/build/BUILD/percolator-rel-3-06-04/converters
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_in/13=percolatorInNs ../src/xml/percolator_in.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://per-colator.com/percolator_out/15=percolatorOutNs ../src/xml/percolator_out.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://psidev.info/psi/pi/mzIdentML/1.1=mzIdentML_ns ../src/xml/mzIdentML1.1.0.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/gaml_tandem1.0.xsd
+ xsdcxx cxx-tree --generate-serialization --generate-insertion XDR --generate-extraction XDR --root-element-all --namespace-map http://www.thegpm.org/TANDEM/2011.12.01.1=tandem_ns --namespace-map =tandem_ns --namespace-map http://www.bioml.com/gaml/=gaml_tandem_ns ../src/xml/tandem2011.12.01.1.xsd
+ /usr/bin/make -O -j4 V=1 VERBOSE=1
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -B/builddir/build/BUILD/percolator-rel-3-06-04/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/converters//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
/usr/bin/make  -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/depend
/usr/bin/make  -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/depend
/usr/bin/make  -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake "--color="
/usr/bin/make  -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/build
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/build
/usr/bin/make  -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/build
make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[  5%] Built target generate_perc_xsdfiles
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[  8%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp_base64.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp_base64.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/converters.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 10%] Building CXX object MSToolkit/RAMP/CMakeFiles/RAMP.dir/ramp.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function ‘RAMPREAL* readPeaks(RAMPFILE*, ramp_fileoffset_t)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1698:13: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
 1698 |         int err;
      |             ^~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.h:134,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:34:
In function ‘*strchr’,
    inlined from ‘readPeaks(RAMPFILE*, long)’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: ‘strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |          ~~~~~~~~~~~~~~~~~^~~~~~~~~~
In function ‘readPeaks(RAMPFILE*, long)’:
cc1plus: note: source object is likely at address zero
In function ‘*strchr’,
    inlined from ‘readPeaks(RAMPFILE*, long)’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: ‘strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |          ~~~~~~~~~~~~~~~~~^~~~~~~~~~
In function ‘readPeaks(RAMPFILE*, long)’:
cc1plus: note: source object is likely at address zero
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp: In function ‘rampSelfTest(char*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:2050:12: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
 2050 |     strncpy(buf, filename, sizeof(buf));
      |            ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:2054:12: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
 2054 |     strncpy(buf, filename, sizeof(buf));
      |            ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 14%] Linking CXX static library libRAMP.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/cmake -P CMakeFiles/RAMP.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP && /usr/bin/cmake -E cmake_link_script CMakeFiles/RAMP.dir/link.txt --verbose=1
/usr/bin/ar qc libRAMP.a CMakeFiles/RAMP.dir/ramp_base64.cpp.o CMakeFiles/RAMP.dir/ramp.cpp.o
/usr/bin/ranlib libRAMP.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 14%] Built target RAMP
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 16%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-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-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.H:28,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:16:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In function ‘LazyMatrix* flip_lazy_matrix(LazyMatrix&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:21:30: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
   21 |         for ( uint j = 0 ; j < lm.rows() ; j++ ) {
      |                            ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:22:38: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
   22 |                 for ( uint i = 0 ; i < lm.cols() ; i++ ) {
      |                                    ~~^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In constructor ‘LazyMatrix::LazyMatrix(int, int, sparse_level, FILE*, off_t)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:39:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   39 |     for ( std::size_t i = 0 ; i < nrows ; i++ ) {
      |                               ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:44:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   44 |     for ( std::size_t i = 0 ; i < nrows; i++ ) {
      |                               ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In copy constructor ‘LazyMatrix::LazyMatrix(const self&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:56:6: warning: value computed is not used [-Wunused-value]
   56 |      *data_copies++;
      |      ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::copy_m_flip(const self&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:67:28: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare]
   67 |       for ( uint i = 0 ; i < x.nrows ; i++ ) {
      |                          ~~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::set_col(std::vector<float>&, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:150:39: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  150 |           for ( std::size_t i = 0 ; i < nrows ; i++ ) {
      |                                     ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::_get_row_retain(std::vector<float>&, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:179:43: warning: variable ‘b’ set but not used [-Wunused-but-set-variable]
  179 |              std::vector<float>::iterator b = this->m[static_cast<std::size_t>(i)]->begin();
      |                                           ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_cols(int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:290:72: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  290 |           for ( std::size_t i = static_cast<std::size_t>(start_idx); i < stop_idx ; i++ ) {
      |                                                                      ~~^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_start_cols(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:298:39: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  298 |           for ( std::size_t i = 0 ; i < rows() ; i++ ) {
      |                                     ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::remove_stop_cols(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:305:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  305 |           for ( std::size_t i =0 ; i < rows() ; i++ ) {
      |                                    ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::column_shift(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:369:23: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  369 |   for ( uint i = 0 ;i < rows() ; i++ ) {
      |                     ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:370:26: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  370 |     for ( uint j = 0 ; j < cols() ; j++ ) {
      |                        ~~^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:373:21: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  373 |       if ( dest_idx >= cols() ) break;
      |            ~~~~~~~~~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp: In member function ‘void LazyMatrix::linear_shift(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:389:25: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  389 |     for ( uint i = 0; i < shift ; i++ ) {
      |                       ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:393:62: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  393 |     for ( std::size_t i = static_cast<std::size_t>(shift); i < nrows; i++ ) {
      |                                                            ~~^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:409:31: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
igned int’} and ‘int’ [-Wsign-compare]
  409 |     for ( uint i = offset ; i < nrows - static_cast<int>(offset); i++ ) {
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/LazyMatrix.cpp:412:76: warning: comparison of integer expressions of different signedness: ‘uint’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
  412 |     for ( uint i = static_cast<uint>(nrows - static_cast<int>(offset)) ; i < nrows; i++ ) {
      |                                                                          ~~^~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 17%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/MSConvertFile.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 19%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSObject.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/MSObject.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 21%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSReader.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::writeFile(const char*, bool, MSObject&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:509:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  509 |   for(unsigned int j=0;j<m.size();j++){
      |                        ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::writeSqlite(const char*, MSObject&, char*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:634:34: warning: the address of ‘MSHeader::header’ will never be NULL [-Waddress]
  634 |       if(m.getHeader().header[i] != 0)
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.h:4,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.h:4,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSToolkitTypes.h:54:14: note: ‘MSHeader::header’ declared here
   54 |         char header[16][128];
      |              ^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::appendFile(Spectrum&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:750:7: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
  750 |   int err;
      |       ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:756:17: warning: variable ‘sizeM’ set but not used [-Wunused-but-set-variable]
  756 |   unsigned long sizeM;
      |                 ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:757:17: warning: variable ‘sizeI’ set but not used [-Wunused-but-set-variable]
  757 |   unsigned long sizeI;
      |                 ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::appendFile(char*, MSObject&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1016:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1016 |       for(i=0;i<m.size();i++) writeTextSpec(fileOut,m.at(i));
      |               ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1025:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1025 |       for(i=0;i<m.size();i++){
      |               ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1034:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1034 |       for(i=0;i<m.size();i++){
      |               ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1043:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1043 |       for(i=0;i<m.size();i++){
      |               ~^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘bool MSReader::executeSqlStmt(Spectrum&, char*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1187:7: warning: unused variable ‘charge’ [-Wunused-variable]
 1187 |   int charge=-1;
      |       ^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘void MSReader::writeCompressSpec(FILE*, Spectrum&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1610:13: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
 1610 |         int err;
      |             ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1616:23: warning: variable ‘sizeM’ set but not used [-Wunused-but-set-variable]
 1616 |         unsigned long sizeM;
      |                       ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:1617:23: warning: variable ‘sizeI’ set but not used [-Wunused-but-set-variable]
 1617 |         unsigned long sizeI;
      |                       ^~~~~
In file included from /usr/include/stdio.h:980,
                 from /usr/include/c++/14/cstdio:42,
                 from /usr/include/c++/14/parallel/compiletime_settings.h:33,
                 from /usr/include/c++/14/parallel/parallel.h:37,
                 from /usr/include/c++/14/parallel/base.h:40,
                 from /usr/include/c++/14/parallel/algobase.h:40,
                 from /usr/include/c++/14/bits/stl_algobase.h:2330,
                 from /usr/include/c++/14/vector:62,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.h:5:
In function ‘sprintf’,
    inlined from ‘MSReader::appendFile(Spectrum&)’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:869:11:
/usr/include/bits/stdio2.h:30:34: warning: ‘lastScanID’ may be used uninitialized [-Wmaybe-uninitialized]
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp: In member function ‘MSReader::appendFile(Spectrum&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSReader.cpp:853:7: note: ‘lastScanID’ was declared here
  853 |   int lastScanID;
      |       ^~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 23%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/MSSingleScan.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 25%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/MSTAllRT.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSTAllRT.cpp: In function ‘int main(int, char**)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSTAllRT.cpp:26:22: warning: variable ‘ff’ set but not used [-Wunused-but-set-variable]
   26 |         MSFileFormat ff;
      |                      ^~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 26%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/MSTDemo.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[  3%] Building CXX object CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/converters/percolator_in.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 28%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/MSWarper.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/MSWarper.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSWarper.cpp:16:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/MSWarper.cpp:17:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable]
  594 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable]
  697 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  806 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  807 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function]
  808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:809:16: warning: ‘msmat* test_msmat(int, char**)’ declared ‘static’ but never defined [-Wunused-function]
  809 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:812:13: warning: ‘void output_bp_chrom(msmat&, char*)’ declared ‘static’ but never defined [-Wunused-function]
  812 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:813:17: warning: ‘msmat* msmat_from_fh(FILE*, sparse_level)’ declared ‘static’ but never defined [-Wunused-function]
  813 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:814:16: warning: ‘msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)’ declared ‘static’ but never defined [-Wunused-function]
  814 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
      |                ^~~~~~~~~~~~~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 32%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/Spectrum.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/Spectrum.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.cpp: In member function ‘bool Spectrum::getRawFilter(char*, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/Spectrum.cpp:282:8: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  282 |   if(sz<strlen(rawFilter)) {
      |      ~~^~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 30%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 35%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 37%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 39%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 41%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 42%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx: In constructor ‘parser_impl::parser_impl()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:106:33: warning: ‘parser_impl::gp_’ will be initialized after [-Wreorder]
  106 |   std::auto_ptr<XMLGrammarPool> gp_; // (new XMLGrammarPoolImpl (mm));
      |                                 ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:102:22: warning:   ‘xercesc_3_2::DOMImplementation& parser_impl::dom_impl_’ [-Wreorder]
  102 |   DOMImplementation& dom_impl_;
      |                      ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:144:1: warning:   when initialized here [-Wreorder]
  144 | parser_impl::parser_impl() : clean_(true),
      | ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx: In member function ‘xsd::cxx::xml::dom::auto_ptr<xercesc_3_2::DOMDocument> parser_impl::start(std::istream&, const std::string&, bool, std::string, std::string, std::string, std::string, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:178:14: warning: unused variable ‘n’ [-Wunused-variable]
  178 |       size_t n(s.size());
      |              ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx:170:9: warning: unused variable ‘i’ [-Wunused-variable]
  170 |     int i(1);
      |         ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 44%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[  7%] Building CXX object CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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_out.cxx.o -MF CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o.d -o CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/converters/percolator_out.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 46%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 50%] Building CXX object CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o
/usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o -MF CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o.d -o CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 51%] Linking CXX static library libperclibrary_part.a
/usr/bin/cmake -P CMakeFiles/perclibrary_part.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/perclibrary_part.dir/link.txt --verbose=1
/usr/bin/ar qc libperclibrary_part.a CMakeFiles/perclibrary_part.dir/percolator_in.cxx.o CMakeFiles/perclibrary_part.dir/percolator_out.cxx.o "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Option.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Enzyme.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Globals.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MassHandler.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/serializer.cxx.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/parser.cxx.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/Logger.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/MyException.cpp.o" "CMakeFiles/perclibrary_part.dir/builddir/build/BUILD/percolator-rel-3-06-04/src/TmpDir.cpp.o"
/usr/bin/ranlib libperclibrary_part.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 55%] Built target perclibrary_part
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 57%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_base.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/msmat_base.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.cpp:16:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 58%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.H:20,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:19:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:20:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable]
  594 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable]
  697 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp: In member function ‘int msmat_header_parser::read_header(msmat*, FILE*, bool, int*)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:92:14: warning: unused variable ‘should_be_semi’ [-Wunused-variable]
   92 |         char should_be_semi = (char)fgetc(header_fh);
      |              ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp: In member function ‘void msmat_header_parser::load_strmap_from_str(std::map<std::__cxx11::basic_string<char>, float>&, const char*, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:361:38: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  361 |   for ( std::size_t i = c1_loc+1 ; i < key_last+1 ; i++ ) {
      |                                    ~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:14: warning: unused variable ‘key_fields_len’ [-Wunused-variable]
  343 |   int c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |              ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:30: warning: unused variable ‘key_last_loc’ [-Wunused-variable]
  343 |   int c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |                              ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:343:44: warning: unused variable ‘key_data_len’ [-Wunused-variable]
  343 |   int c2_loc,key_fields_len, key_last_loc, key_data_len, key_len, val_len;
      |                                            ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:344:8: warning: unused variable ‘key_len_data’ [-Wunused-variable]
  344 |   char key_len_data[128], val_len_data[128];
      |        ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:344:27: warning: unused variable ‘val_len_data’ [-Wunused-variable]
  344 |   char key_len_data[128], val_len_data[128];
      |                           ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:359:7: warning: unused variable ‘key_data_idx’ [-Wunused-variable]
  359 |   int key_data_idx;
      |       ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  806 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  807 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function]
  808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:809:16: warning: ‘msmat* test_msmat(int, char**)’ declared ‘static’ but never defined [-Wunused-function]
  809 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:812:13: warning: ‘void output_bp_chrom(msmat&, char*)’ declared ‘static’ but never defined [-Wunused-function]
  812 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:813:17: warning: ‘msmat* msmat_from_fh(FILE*, sparse_level)’ declared ‘static’ but never defined [-Wunused-function]
  813 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:814:16: warning: ‘msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)’ declared ‘static’ but never defined [-Wunused-function]
  814 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
      |                ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp: In member function ‘msmat_header_parser::load_map_from_str(std::map<float, float, std::less<float>, std::allocator<std::pair<float const, float> > >&, char const*, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:314:10: warning: ‘operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  314 |   delete k;
      |          ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:306:48: note: returned from ‘operator new[](unsigned long)’
  306 |   flt_map_type * k = new flt_map_type[num_items];
      |                                                ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:315:10: warning: ‘operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  315 |   delete v;
      |          ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:307:48: note: returned from ‘operator new[](unsigned long)’
  307 |   flt_map_type * v = new flt_map_type[num_items];
      |                                                ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/convertmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
ers/MSToolkit/msmat_header_parser.cpp: In member function ‘msmat_header_parser::load_strmap_from_str(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, float, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, float> > >&, char const*, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:386:10: warning: ‘operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  386 |   delete values;
      |          ^~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_header_parser.cpp:381:37: note: returned from ‘operator new[](unsigned long)’
  381 |   float * values = new float[val_len];
      |                                     ^
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 60%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat_test.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp:4:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable]
  594 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable]
  697 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp: In function ‘int main(int, char**)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_test.cpp:13:12: warning: unused variable ‘m’ [-Wunused-variable]
   13 |   msmat  * m;
      |            ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  806 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  807 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function]
  808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:809:16: warning: ‘msmat* test_msmat(int, char**)’ declared ‘static’ but never defined [-Wunused-function]
  809 | static msmat * test_msmat(int argc, char ** argv);
      |                ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:812:13: warning: ‘void output_bp_chrom(msmat&, char*)’ declared ‘static’ but never defined [-Wunused-function]
  812 | static void output_bp_chrom( msmat & m , char * fname);
      |             ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:813:17: warning: ‘msmat* msmat_from_fh(FILE*, sparse_level)’ declared ‘static’ but never defined [-Wunused-function]
  813 | static msmat *  msmat_from_fh ( FILE * msmat_file, sparse_level s = LM_FULL_DATA );
      |                 ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:814:16: warning: ‘msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)’ declared ‘static’ but never defined [-Wunused-function]
  814 | static msmat * msmat_from_thevoid ( const std::vector<float> & mzs, const std::vector<float> & rts, std::vector < std::vector< float > > & chroms , bool as_scans = true );
      |                ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 33%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/crawutils.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:21:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘void crawutils::rankties(std::vector<float>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:261:9: warning: unused variable ‘start_idx’ [-Wunused-variable]
  261 |     int start_idx = -1;
      |         ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:262:9: warning: unused variable ‘stop_idx’ [-Wunused-variable]
  262 |     int stop_idx = -1;
      |         ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘void crawutils::rank_by_pos_ties(const std::vector<std::pair<float, int> >&, std::vector<float>&, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:354:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<float, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  354 |       if ( ( i != (sorted_by_i.size() ) ) && ( sorted_by_i[static_cast<std::size_t>(i)].first == last_val) ) {
      |              ~~^~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:346:9: warning: unused variable ‘last_rank’ [-Wunused-variable]
  346 |     int last_rank = -1;
      |         ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘float crawutils::spectra_spearman_rank_corr_3(const std::vector<float>&, const std::vector<float>&, double, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:455:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  455 |     for ( std::size_t i = 0 ; i < (int)s1.size();  i++ ) {
      |                               ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘float crawutils::spectra_spearman_rank_corr_4(const std::vector<float>&, const std::vector<float>&, double, double)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:488:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  488 |     for ( std::size_t i = 0 ; i < (int)s1.size();  i++ ) {
      |                               ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘int crawutils::idx_of_centroid(const std::vector<float>&, const std::vector<float>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:976:23: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  976 |     for (idx = 1; idx < (int)y.size(); idx++)
      |                   ~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘int crawutils::tryptic_digester_proto(std::string, std::vector<std::__cxx11::basic_string<char> >&, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:1090:10: warning: unused variable ‘last_tryp’ [-Wunused-variable]
 1090 |     bool last_tryp = false;
      |          ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp: In function ‘float crawstats::pi0_from_StoreySplineFit(const std::vector<std::pair<float, float> >&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.cpp:1402:29: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1402 |   for (std::size_t i = 1; i <= n - 1; i++)
      |                           ~~^~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 48%] Building CXX object MSToolkit/CMakeFiles/MSToolkit.dir/msmat.cpp.o
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/g++ -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MSToolkit/msmat.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /usr/include/boost/math/special_functions/beta.hpp:13,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/crawutils.H:38,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:24,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:48,
                 from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:17:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_scans::msmat_scans()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:594:15: warning: unused variable ‘a’ [-Wunused-variable]
  594 |           int a = 3;
      |               ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: In constructor ‘msmat_chroms::msmat_chroms()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:697:9: warning: unused variable ‘a’ [-Wunused-variable]
  697 |     int a  = 3;
      |         ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In constructor ‘transition_manager::transition_manager(std::vector<transition_info>)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:47:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<transition_info>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   47 |       for ( int  i = 0 ; i < transitions.size() ; i++ ) {
      |                          ~~^~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::init_transitions_from_labels()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:76:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   76 |    for ( int i = 0 ; i < labels.size() ; i++ ) {
      |                      ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::tabular_input(std::ifstream&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:107:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  107 |      for ( int mz_idx = 0 ; mz_idx < this->get_num_mzs() ; mz_idx++ ) {
      |                             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::zero_chrom(int, int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:185:70: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  185 |   for ( std::size_t i = static_cast<std::size_t>(start_scan_idx) ; i <= stop_scan_idx ; i++ ) {
      |                                                                    ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::retain_dist_set(int, std::vector<int>&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:216:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  216 |     for ( int i = 0 ; i < this->get_num_rts() ; i++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::retain_chrom_set(int, std::vector<std::pair<int, int> >&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:225:9: warning: unused variable ‘set_idx’ [-Wunused-variable]
  225 |     int set_idx = 0;
      |         ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::retain_chrom(int, int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:251:31: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  251 |   for ( std::size_t i = 0 ; i < start_scan_idx ; i++ ) {
      |                             ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘int msmat::check_size_from_position() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:271:30: warning: comparison of integer expressions of different signedness: ‘off64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  271 |   if ( ( end_pos - cur_pos ) == get_num_mzs() * get_num_rts() * sizeof(float) ) {
      |        ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::calc_bp_chrom()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:668:36: warning: variable ‘scan_length’ set but not used [-Wunused-but-set-variable]
  668 |   std::size_t scan_idx, num_scans, scan_length;
      |                                    ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::pad_start_stop(int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:775:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  775 |                                   for ( int i = stop_mapped_coord+1 ; i < get_num_rts()  ; i++  ) {
      |                                                                       ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::time_interpolate(double, msmat&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1056:14: warning: variable ‘dim’ set but not used [-Wunused-but-set-variable]
 1056 |   matrix_dim dim = get_data_dim();
      |              ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::get_median() const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1266:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1266 |   for ( int i = 0 ; i < this->get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1267:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1267 |     for ( int j = 0 ; j < this->get_num_cols() ; j++ ) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::get_avg(int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/srmake[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
c/converters/MSToolkit/msmat.cpp:1282:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1282 |     if ( i < 0 || i >= get_num_rts()  ) {
      |                   ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::calc_twomat_num(const msmat&, double, double, int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1313:72: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1313 |                                      for ( int self_idx = 0 ; self_idx < get_num_rts() ; self_idx++ ) {
      |                                                               ~~~~~~~~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1315:72: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1315 |                                        if ( other_idx < 0 || other_idx >= other.get_num_rts() ) {
      |                                                              ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::calc_mat_denom(double, int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1338:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1338 |     if ( i < 0 || i >= get_num_rts() ) {
      |                   ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::correlation_w_shift(const msmat&, int) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1356:17: warning: unused variable ‘self’ [-Wunused-variable]
 1356 |   const msmat & self = *this;
      |                 ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘msmat_chroms* msmat_chroms::extract_mzidx_range(int, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1411:33: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1411 |     for ( std::size_t i = 0;  i < r_stop - r_start ; i++ ) {
      |                               ~~^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1410:9: warning: unused variable ‘foo’ [-Wunused-variable]
 1410 |     int foo = 5;
      |         ^~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘virtual void msmat_scans::get_chrom(int, std::vector<float>&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1486:11: warning: unused variable ‘volatile_this’ [-Wunused-variable]
 1486 |   msmat * volatile_this;
      |           ^~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In function ‘msmat* test_msmat(int, char**)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1593:19: warning: variable ‘ti_file’ set but not used [-Wunused-but-set-variable]
 1593 |   FILE * o_file, *ti_file, *sg_file;
      |                   ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1593:29: warning: variable ‘sg_file’ set but not used [-Wunused-but-set-variable]
 1593 |   FILE * o_file, *ti_file, *sg_file;
      |                             ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_mzs_by_avg(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1816:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1816 |     new_cnt < mzs.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1818:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1818 |       for ( std::size_t i = 0 ; i < decimate_size ; i++ ) {
      |                                 ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_rts_by_avg(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1846:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1846 |     new_cnt < rts.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1848:35: warning: comparison of integer expressions of different signedness: ‘std::size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
 1848 |       for ( std::size_t i = 0 ; i < decimate_size ; i++ ) {
      |                                 ~~^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_mzs_by_sample(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1868:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1868 |     new_cnt < mzs.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::decimate_rts_by_sample(int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1886:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<float>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1886 |     new_cnt < rts.size() ;
      |     ~~~~~~~~^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘bool msmat::equals_data(const msmat&, double) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1909:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1909 |   for ( int i = 0 ; i < get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘double msmat::sum_abs_diffs(const msmat&) const’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1932:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
 1932 |   for ( int i = 0 ; i < get_num_rows() ; i++ ) {
      |                     ~~^~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1929:10: warning: unused variable ‘nrows’ [-Wunused-variable]
 1929 |   size_t nrows = get_num_rows();
      |          ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void msmat::tabular_output(std::ostream&, int, int, int, int, bool, char)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1978:13: warning: unused variable ‘num_mzs’ [-Wunused-variable]
 1978 |   const int num_mzs = static_cast<int>(get_num_mzs());
      |             ^~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp: In member function ‘void ttest_score_matrix::unmask_search(msmat::mz_type, msmat::rt_type, msmat::rt_type)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:2097:7: warning: unused variable ‘start_rt_idx’ [-Wunused-variable]
 2097 |   int start_rt_idx = this->rt_to_rtidx(start_rt);
      |       ^~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:2098:7: warning: unused variable ‘stop_rt_idx’ [-Wunused-variable]
 2098 |   int stop_rt_idx = this->rt_to_rtidx(stop_rt);
      |       ^~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H: At global scope:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:806:12: warning: ‘int test_msmat_time_interp(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  806 | static int test_msmat_time_interp( msmat * msmat_f );
      |            ^~~~~~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:807:12: warning: ‘int test_msmat_sg_test(msmat*)’ declared ‘static’ but never defined [-Wunused-function]
  807 | static int test_msmat_sg_test( msmat * msmat_fh);
      |            ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.H:808:12: warning: ‘int test_msmat_output(msmat*, char*)’ declared ‘static’ but never defined [-Wunused-function]
  808 | static int test_msmat_output ( msmat * msmat_fh, char * out_fname);
      |            ^~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1728:9: warning: ‘msmat* msmat_from_thevoid(const std::vector<float>&, const std::vector<float>&, std::vector<std::vector<float> >&, bool)’ defined but not used [-Wunused-function]
 1728 | msmat * msmat_from_thevoid
      |         ^~~~~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1701:6: warning: ‘void output_bp_chrom(msmat&, char*)’ defined but not used [-Wunused-function]
 1701 | void output_bp_chrom( msmat & m, char * fname  ) {
      |      ^~~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat.cpp:1570:9: warning: ‘msmat* test_msmat(int, char**)’ defined but not used [-Wunused-function]
 1570 | msmat * test_msmat ( int argc , char ** argv ) {
      |         ^~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/msmat_base.H:69:21: warning: ‘valid_fields’ defined but not used [-Wunused-variable]
   69 | const static char * valid_fields[] = {
      |                     ^~~~~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 66%] Linking CXX static library libMSToolkit.a
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/cmake -P CMakeFiles/MSToolkit.dir/cmake_clean_target.cmake
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/MSToolkit.dir/link.txt --verbose=1
/usr/bin/ar qc libMSToolkit.a CMakeFiles/MSToolkit.dir/LazyMatrix.cpp.o CMakeFiles/MSToolkit.dir/MSConvertFile.cpp.o CMakeFiles/MSToolkit.dir/MSObject.cpp.o CMakeFiles/MSToolkit.dir/MSReader.cpp.o CMakeFiles/MSToolkit.dir/MSSingleScan.cpp.o CMakeFiles/MSToolkit.dir/MSTAllRT.cpp.o CMakeFiles/MSToolkit.dir/MSTDemo.cpp.o CMakeFiles/MSToolkit.dir/MSWarper.cpp.o CMakeFiles/MSToolkit.dir/Spectrum.cpp.o CMakeFiles/MSToolkit.dir/crawutils.cpp.o CMakeFiles/MSToolkit.dir/msmat.cpp.o CMakeFiles/MSToolkit.dir/msmat_base.cpp.o CMakeFiles/MSToolkit.dir/msmat_header_parser.cpp.o CMakeFiles/MSToolkit.dir/msmat_test.cpp.o
/usr/bin/ranlib libMSToolkit.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 66%] Built target MSToolkit
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 12%] 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-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/converters/mzIdentML1.1.0.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 67%] Building CXX object CMakeFiles/converters.dir/Reader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/Reader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 69%] Building CXX object CMakeFiles/converters.dir/SqtReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/SqtReader.cpp.o -MF CMakeFiles/converters.dir/SqtReader.cpp.o.d -o CMakeFiles/converters.dir/SqtReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/SqtReader.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 64%] Building CXX object 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-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/converters/tandem2011.12.01.1.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 62%] Building CXX object CMakeFiles/converters.dir/gaml_tandem1.0.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-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/gaml_tandem1.0.cxx.o -MF CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o.d -o CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o -c /builddir/build/BUILD/percolator-rel-3-06-04/converters/gaml_tandem1.0.cxx
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 71%] Building CXX object CMakeFiles/converters.dir/MzidentmlReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/MzidentmlReader.cpp.o -MF CMakeFiles/converters.dir/MzidentmlReader.cpp.o.d -o CMakeFiles/converters.dir/MzidentmlReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MzidentmlReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MzidentmlReader.cpp: In member function ‘virtual void MzidentmlReader::getMaxMinCharge(const std::string&, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MzidentmlReader.cpp:86:30: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=]
   86 |   } catch (ifstream::failure e) {
      |                              ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MzidentmlReader.cpp:94:24: warning: catching polymorphic type ‘class MyException’ by value [-Wcatch-value=]
   94 |   } catch (MyException e) {
      |                        ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MzidentmlReader.cpp:97:27: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
   97 |   } catch (std::exception e) {
      |                           ^
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 73%] Building CXX object CMakeFiles/converters.dir/SequestReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/SequestReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/SequestReader.cpp: In member function ‘virtual void SequestReader::createPSM(const mzIdentML_ns::SpectrumIdentificationItemType&, percolatorInNs::fragSpectrumScan::experimentalMass_type, bool, unsigned int, boost::shared_ptr<FragSpectrumScanDatabase>, const std::string&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/SequestReader.cpp:169:12: warning: unused variable ‘PI’ [-Wunused-variable]
  169 |     double PI = boost::lexical_cast<double>(item.calculatedPI().get());
      |            ^~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/SequestReader.cpp:174:14: warning: unused variable ‘peptide_length’ [-Wunused-variable]
  174 |     unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
      |              ^~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 78%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/FragSpectrumScanDatabase.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabase.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabase.cpp: In member function ‘std::string FragSpectrumScanDatabase::decoratePeptide(const percolatorInNs::peptideType&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabase.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   81 |     if (it->first <= peptideSeq.length()) {
      |         ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 76%] Building CXX object CMakeFiles/converters.dir/TandemReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/TandemReader.cpp.o -MF CMakeFiles/converters.dir/TandemReader.cpp.o.d -o CMakeFiles/converters.dir/TandemReader.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp: In member function ‘virtual void TandemReader::getMaxMinCharge(const std::string&, bool)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp:248:24: warning: catching polymorphic type ‘class MyException’ by value [-Wcatch-value=]
  248 |   } catch (MyException e) {
      |                        ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp:251:27: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
  251 |   } catch (std::exception e) {
      |                           ^
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp: In member function ‘void TandemReader::createPSM(const tandem_ns::peptide::domain_type&, double, unsigned int, double, double, bool, boost::shared_ptr<FragSpectrumScanDatabase>, const peptideProteinMapType&, const std::string&, int)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/TandemReader.cpp:468:29: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  468 |     f_seq.push_back( charge == c ? 1.0 : 0.0);
      |                      ~~~~~~~^~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 75%] Building CXX object CMakeFiles/converters.dir/MsgfplusReader.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/MsgfplusReader.cpp
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp: In member function ‘virtual void MsgfplusReader::createPSM(const mzIdentML_ns::SpectrumIdentificationItemType&, percolatorInNs::fragSpectrumScan::experimentalMass_type, bool, unsigned int, boost::shared_ptr<FragSpectrumScanDatabase>, const std::string&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:332:27: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
  332 |                           else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
      |                           ^~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:332:104: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’
  332 |                           else StdevErrorTop7 = boost::lexical_cast<double>(up.value().get().c_str()); break;
      |                                                                                                        ^~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:271:14: warning: unused variable ‘peptide_length’ [-Wunused-variable]
  271 |     unsigned peptide_length = peptideLength(peptideSeqWithFlanks);
      |              ^~~~~~~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MsgfplusReader.cpp:290:12: warning: variable ‘SpecEValue’ set but not used [-Wunused-but-set-variable]
  290 |     double SpecEValue = 0.0;
      |            ^~~~~~~~~~
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 82%] Building CXX object CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/FragSpectrumScanDatabaseTokyodb.cpp.o -MF CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o.d -o CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp: In member function ‘virtual void FragSpectrumScanDatabaseTokyoDB::putFSS(percolatorInNs::fragSpectrumScan&)’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/FragSpectrumScanDatabaseTokyodb.cpp:165:10: warning: unused variable ‘valueSize’ [-Wunused-variable]
  165 |   size_t valueSize(buf.size ());
      |          ^~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 80%] Building CXX object CMakeFiles/converters.dir/Interface.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/Interface.cpp.o -MF CMakeFiles/converters.dir/Interface.cpp.o.d -o CMakeFiles/converters.dir/Interface.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
In file included from /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.cpp:18:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.h: In constructor ‘Interface::Interface()’:
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.h:50:14: warning: ‘Interface::xmlOutput’ will be initialized after [-Wreorder]
   50 |         bool xmlOutput;
      |              ^~~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.h:47:21: warning:   ‘std::string Interface::outputFN’ [-Wreorder]
   47 |         std::string outputFN;
      |                     ^~~~~~~~
/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Interface.cpp:21:1: warning:   when initialized here [-Wreorder]
   21 | Interface::Interface() : xmlOutput(false), outputFN("") { }
      | ^~~~~~~~~
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 83%] Linking CXX static library libconverters.a
/usr/bin/cmake -P CMakeFiles/converters.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/converters.dir/link.txt --verbose=1
/usr/bin/ar qc libconverters.a CMakeFiles/converters.dir/mzIdentML1.1.0.cxx.o CMakeFiles/converters.dir/gaml_tandem1.0.cxx.o CMakeFiles/converters.dir/tandem2011.12.01.1.cxx.o CMakeFiles/converters.dir/Reader.cpp.o CMakeFiles/converters.dir/SqtReader.cpp.o CMakeFiles/converters.dir/MzidentmlReader.cpp.o CMakeFiles/converters.dir/SequestReader.cpp.o CMakeFiles/converters.dir/MsgfplusReader.cpp.o CMakeFiles/converters.dir/TandemReader.cpp.o CMakeFiles/converters.dir/FragSpectrumScanDatabase.cpp.o CMakeFiles/converters.dir/Interface.cpp.o CMakeFiles/converters.dir/FragSpectrumScanDatabaseTokyodb.cpp.o
/usr/bin/ranlib libconverters.a
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 89%] Built target converters
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/depend
/usr/bin/make  -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend
/usr/bin/make  -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build
/usr/bin/make  -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 94%] Building CXX object CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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/sqt2pin.dir/Sqt2Pin.cpp.o -MF CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o.d -o CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -c /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/Sqt2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 94%] Building CXX object CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/Tandem2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 91%] Building CXX object CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o
/usr/bin/g++ -DBOOST_ATOMIC_NO_LIB -DBOOST_FILESYSTEM_NO_LIB -DBOOST_SYSTEM_NO_LIB -DXML_SUPPORT -D__TOKYODB__ -I/usr/include/tirpc -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src -I/builddir/build/BUILD/percolator-rel-3-06-04/converters -I/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -std=c++14 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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-rel-3-06-04/src/converters/Msgfplus2Pin.cpp
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro    -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc -rdynamic CMakeFiles/sqt2pin.dir/Sqt2Pin.cpp.o -o sqt2pin   -L/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src  libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltirpc -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
In function ‘strchr’,
    inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: ‘__builtin_strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function ‘readPeaks’:
lto1: note: source object is likely at address zero
In function ‘strchr’,
    inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: ‘__builtin_strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function ‘readPeaks’:
lto1: note: source object is likely at address zero
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[100%] Built target sqt2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[100%] Linking CXX executable 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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro    -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc -rdynamic CMakeFiles/msgf2pin.dir/Msgfplus2Pin.cpp.o -o msgf2pin   -L/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src  libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltirpc -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
In function ‘strchr’,
    inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: ‘__builtin_strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function ‘readPeaks’:
lto1: note: source object is likely at address zero
In function ‘strchr’,
    inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: ‘__builtin_strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function ‘readPeaks’:
lto1: note: source object is likely at address zero
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[100%] Built target msgf2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 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,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,-z,relro    -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -ltirpc -rdynamic CMakeFiles/tandem2pin.dir/Tandem2Pin.cpp.o -o tandem2pin   -L/builddir/build/BUILD/percolator-rel-3-06-04/src/converters/../../src  libconverters.a libperclibrary_part.a MSToolkit/libMSToolkit.a -lxerces-c /usr/lib64/libboost_filesystem.a /usr/lib64/libboost_atomic.a /usr/lib64/libboost_system.a -ltirpc -ltokyocabinet -lbz2 -lz -lsqlite3 MSToolkit/RAMP/libRAMP.a -ldl 
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
In function ‘strchr’,
    inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1599:35:
/usr/include/string.h:241:27: warning: ‘__builtin_strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function ‘readPeaks’:
lto1: note: source object is likely at address zero
In function ‘strchr’,
    inlined from ‘readPeaks’ at /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/ramp.cpp:1613:35:
/usr/include/string.h:241:27: warning: ‘__builtin_strchr’ reading 1 or more bytes from a region of size 0 [-Wstringop-overread]
  241 |   return __builtin_strchr (__s, __c);
      |                           ^
In function ‘readPeaks’:
lto1: note: source object is likely at address zero
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles 0
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.vMzpVQ
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64
++ dirname /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64
+ 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=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro    -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd percolator-rel-3-06-04
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64 'INSTALL=/usr/bin/install -p' -C percolator
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04 -B/builddir/build/BUILD/percolator-rel-3-06-04/percolator --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/percolator//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/perclibrary.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/CMakeFiles/perclibrary.dir/build.make src/CMakeFiles/perclibrary.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'src/CMakeFiles/perclibrary.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 54%] Built target perclibrary
/usr/bin/make  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/picked_protein/CMakeFiles/picked_protein.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/picked_protein/CMakeFiles/picked_protein.dir/build.make src/picked_protein/CMakeFiles/picked_protein.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'src/picked_protein/CMakeFiles/picked_protein.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 68%] Built target picked_protein
/usr/bin/make  -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/blas/CMakeFiles/blas.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/blas/CMakeFiles/blas.dir/build.make src/blas/CMakeFiles/blas.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'src/blas/CMakeFiles/blas.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 75%] Built target blas
/usr/bin/make  -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/fido/CMakeFiles/fido.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/fido/CMakeFiles/fido.dir/build.make src/fido/CMakeFiles/fido.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'src/fido/CMakeFiles/fido.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 84%] Built target fido
/usr/bin/make  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/CMakeFiles/percolator.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/CMakeFiles/percolator.dir/build.make src/CMakeFiles/percolator.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'src/CMakeFiles/percolator.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 87%] Built target percolator
/usr/bin/make  -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality /builddir/build/BUILD/percolator-rel-3-06-04/percolator/src/qvality/CMakeFiles/qvality.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f src/qvality/CMakeFiles/qvality.dir/build.make src/qvality/CMakeFiles/qvality.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'src/qvality/CMakeFiles/qvality.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[ 89%] Built target qvality
/usr/bin/make  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
cd /builddir/build/BUILD/percolator-rel-3-06-04/percolator && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04 /builddir/build/BUILD/percolator-rel-3-06-04/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator /builddir/build/BUILD/percolator-rel-3-06-04/percolator/tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/make  -f tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build.make tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[2]: Nothing to be done for 'tests/unit_tests/percolator/CMakeFiles/gtest_unit.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
[100%] Built target gtest_unit
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/percolator/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/xml/percolator/xml-pin-1-3/percolator_in.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/xml/percolator/xml-pout-1-5/percolator_out.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/bin/percolator
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/bin/qvality
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/./bin/gtest_unit
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/percolator'
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64 'INSTALL=/usr/bin/install -p' -C converters
make: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/cmake -S/builddir/build/BUILD/percolator-rel-3-06-04/src/converters -B/builddir/build/BUILD/percolator-rel-3-06-04/converters --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles /builddir/build/BUILD/percolator-rel-3-06-04/converters//CMakeFiles/progress.marks
/usr/bin/make  -f CMakeFiles/Makefile2 all
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/perclibrary_part.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/perclibrary_part.dir/build.make CMakeFiles/perclibrary_part.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/perclibrary_part.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 25%] Built target perclibrary_part
/usr/bin/make  -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/generate_perc_xsdfiles.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/generate_perc_xsdfiles.dir/build.make CMakeFiles/generate_perc_xsdfiles.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/generate_perc_xsdfiles.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 28%] Built target generate_perc_xsdfiles
/usr/bin/make  -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/converters.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/converters.dir/build.make CMakeFiles/converters.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/converters.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 57%] Built target converters
/usr/bin/make  -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/RAMP/CMakeFiles/RAMP.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f MSToolkit/RAMP/CMakeFiles/RAMP.dir/build.make MSToolkit/RAMP/CMakeFiles/RAMP.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'MSToolkit/RAMP/CMakeFiles/RAMP.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 62%] Built target RAMP
/usr/bin/make  -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit /builddir/build/BUILD/percolator-rel-3-06-04/converters/MSToolkit/CMakeFiles/MSToolkit.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f MSToolkit/CMakeFiles/MSToolkit.dir/build.make MSToolkit/CMakeFiles/MSToolkit.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'MSToolkit/CMakeFiles/MSToolkit.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 89%] Built target MSToolkit
/usr/bin/make  -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/msgf2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/msgf2pin.dir/build.make CMakeFiles/msgf2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/msgf2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 92%] Built target msgf2pin
/usr/bin/make  -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/sqt2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/sqt2pin.dir/build.make CMakeFiles/sqt2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/sqt2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[ 96%] Built target sqt2pin
/usr/bin/make  -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/depend
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
cd /builddir/build/BUILD/percolator-rel-3-06-04/converters && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/src/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles/tandem2pin.dir/DependInfo.cmake "--color="
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/make  -f CMakeFiles/tandem2pin.dir/build.make CMakeFiles/tandem2pin.dir/build
make[2]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[2]: Nothing to be done for 'CMakeFiles/tandem2pin.dir/build'.
make[2]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
[100%] Built target tandem2pin
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
/usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/percolator-rel-3-06-04/converters/CMakeFiles 0
/usr/bin/make  -f CMakeFiles/Makefile2 preinstall
make[1]: Entering directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
make[1]: Nothing to be done for 'preinstall'.
make[1]: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/bin/msgf2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/bin/sqt2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/bin/tandem2pin
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/percolator/xml-1-1/mzIdentML1.1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/percolator/xml-2011.12.01.1/gaml_tandem1.0.xsd
-- Installing: /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/percolator/xml-2011.12.01.1/tandem2011.12.01.1.xsd
make: Leaving directory '/builddir/build/BUILD/percolator-rel-3-06-04/converters'
+ mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/lib64/percolator
++ find . -type f '(' -name '*.a' ')'
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libconverters.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/libperclibrary_part.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/libMSToolkit.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./converters/MSToolkit/RAMP/libRAMP.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./fido/libfido.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/libperclibrary.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/picked_protein/libpicked_protein.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/fido/libfido.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/lib64/percolator
+ for i in `find . -type f \( -name "*.a" \)`
+ install -pm 755 ./percolator/src/blas/libblas.a /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/lib64/percolator
+ rm -f /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/bin/gtest_unit
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 3.06.04-3.fc40 --unique-debug-suffix -3.06.04-3.fc40.aarch64 --unique-debug-src-base percolator-3.06.04-3.fc40.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/percolator-rel-3-06-04
find-debuginfo: starting
Extracting debug info from 5 files
DWARF-compressing 5 files
sepdebugcrcfix: Updated 5 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/percolator-3.06.04-3.fc40.aarch64
5448 blocks
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.gd8tNV
+ umask 022
+ cd /builddir/build/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=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro    -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd percolator-rel-3-06-04
+ mkdir -p test
+ pushd test
~/build/BUILD/percolator-rel-3-06-04/test ~/build/BUILD/percolator-rel-3-06-04
+ ../converters/sqt2pin -o pin.tab ../yeast-01.sqt ../yeast-01.shuffled.sqt

Pin-converter version 3.06.4, Build Date Jan 25 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 69742358cb1d499fa62cbbc3e0f55137
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 Jan 25 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 Thu Jan 25 13:30:26 2024
 on 69742358cb1d499fa62cbbc3e0f55137
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 0.4518 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 19.7123 cpu seconds or 9 seconds wall clock time.
+ popd
~/build/BUILD/percolator-rel-3-06-04
~/build/BUILD/percolator-rel-3-06-04/percolator ~/build/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-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) =   0.03 sec
+ popd
~/build/BUILD/percolator-rel-3-06-04
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: percolator-3.06.04-3.fc40.aarch64
Provides: percolator = 3.06.04-3.fc40 percolator(aarch-64) = 3.06.04-3.fc40
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) 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-3.2.so()(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) rtld(GNU_HASH)
Obsoletes: fido-pi = 0:0
Processing files: percolator-data-3.06.04-3.fc40.noarch
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.gXFl1y
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/doc/percolator-data
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/ReadMe.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-README /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/doc/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/doc/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.XWonMw
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/licenses/percolator-data
+ export LC_ALL=
+ LC_ALL=
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/licenses/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/license.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/licenses/percolator-data
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/licenses/percolator-data
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-data = 3.06.04-3.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-static-3.06.04-3.fc40.aarch64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.4QFxji
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ DOCDIR=/builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/doc/percolator-static
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/ReadMe.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-README /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/doc/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/src/converters/MSToolkit/RAMP/RAMP-Readme.Mike.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/doc/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.P0CbZM
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ LICENSEDIR=/builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/licenses/percolator-static
+ export LC_ALL=
+ LC_ALL=
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/licenses/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/license.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/licenses/percolator-static
+ cp -pr /builddir/build/BUILD/percolator-rel-3-06-04/RAMP_license_lgpl-2.1.txt /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64/usr/share/licenses/percolator-static
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: percolator-static = 3.06.04-3.fc40 percolator-static(aarch-64) = 3.06.04-3.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debugsource-3.06.04-3.fc40.aarch64
Provides: percolator-debugsource = 3.06.04-3.fc40 percolator-debugsource(aarch-64) = 3.06.04-3.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: percolator-debuginfo-3.06.04-3.fc40.aarch64
Provides: debuginfo(build-id) = 6a82a456e0d9e852a5238cb22a95be438b2d67f0 debuginfo(build-id) = 6ea9ae8c8ee7b40fb4ef323042291d8fb8d4cabf debuginfo(build-id) = ec002b2e1797cd4b4d4aac176055b48466235ea7 debuginfo(build-id) = f0ee58ee17ffdde805bd5a7977e7c123bd8659e0 debuginfo(build-id) = fbd52a4616eb7a251dc0430a4d0e49b6f42c1f39 percolator-debuginfo = 3.06.04-3.fc40 percolator-debuginfo(aarch-64) = 3.06.04-3.fc40
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: percolator-debugsource(aarch-64) = 3.06.04-3.fc40
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64
Wrote: /builddir/build/RPMS/percolator-debugsource-3.06.04-3.fc40.aarch64.rpm
Wrote: /builddir/build/RPMS/percolator-data-3.06.04-3.fc40.noarch.rpm
Wrote: /builddir/build/RPMS/percolator-3.06.04-3.fc40.aarch64.rpm
Wrote: /builddir/build/RPMS/percolator-static-3.06.04-3.fc40.aarch64.rpm
Wrote: /builddir/build/RPMS/percolator-debuginfo-3.06.04-3.fc40.aarch64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.vGVoX3
+ umask 022
+ cd /builddir/build/BUILD
+ cd percolator-rel-3-06-04
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/percolator-3.06.04-3.fc40.aarch64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.x2mnYi
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf /builddir/build/BUILD/percolator-rel-3-06-04-SPECPARTS
+ rm -rf percolator-rel-3-06-04 percolator-rel-3-06-04.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild percolator-3.06.04-3.fc40.src.rpm
Finish: build phase for percolator-3.06.04-3.fc40.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-aarch64-1706189148.512818/root/var/log/dnf5.log
INFO: Done(/var/lib/copr-rpmbuild/results/percolator-3.06.04-3.fc40.src.rpm) Config(child) 3 minutes 57 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-debuginfo",
            "epoch": null,
            "version": "3.06.04",
            "release": "3.fc40",
            "arch": "aarch64"
        },
        {
            "name": "percolator",
            "epoch": null,
            "version": "3.06.04",
            "release": "3.fc40",
            "arch": "aarch64"
        },
        {
            "name": "percolator-debugsource",
            "epoch": null,
            "version": "3.06.04",
            "release": "3.fc40",
            "arch": "aarch64"
        },
        {
            "name": "percolator-data",
            "epoch": null,
            "version": "3.06.04",
            "release": "3.fc40",
            "arch": "noarch"
        },
        {
            "name": "percolator",
            "epoch": null,
            "version": "3.06.04",
            "release": "3.fc40",
            "arch": "src"
        },
        {
            "name": "percolator-static",
            "epoch": null,
            "version": "3.06.04",
            "release": "3.fc40",
            "arch": "aarch64"
        }
    ]
}
RPMResults finished